I do think that we are in uncharted territory here and I agree with Cristi Stoica that your argument deserves deeper examination, which I don't have the time nor likely the expertise to look at closely. I have wondered about nanomachines and the second law for some time, but I do believe we can appeal for insight to the null result of the grandest experiment of all time together with the result of a not so grand experiment (one done by us mere humans). First let me quote from the Wikipedia Page for "Entropy in Thermodynamics and Information Theory, where the following experiment is cited:
Shoichi Toyabe; Takahiro Sagawa; Masahito Ueda; Eiro Muneyuki; Masaki Sano (2010-09-29). "Information heat engine: converting information to energy by feedback control". Nature Physics 6 (12): 988–992. arXiv:1009.5287. Bibcode:2011NatPh...6..988T. doi:10.1038/nphys1821. "We demonstrated that free energy is obtained by a feedback control using the information about the system; information is converted to free energy, as the first realization of Szilard-type Maxwell’s demon."
Now, let's think about this in-the-laboratory Szilard engine as a thought experiment and note particularly that it definitely scales the possibility of realising a Szilard engine up to the nano-technology, or more importantly, the molecular biology and microbiology scale.
Now for the grandest experiment of all time: the evolution of life on Earth. After 3 billion (and likely more like 4 billion) years of evolution, wherever biologists look, the basic powerhouses driving life (photosynthesis, mitochondrial ATP production from chemical energy ingested by cells and so forth) are well understood and almost certainly universal. It seems to me, that if there were a way around the second law through biological nanomachines (particularly with a variation on the Szilard engine, since the experiment above shows how it can scale to biological systems), evolution would almost certainly have found it by now and this second-law-violating process would be meeting all the needs of the creatures that evolved it. One could imagine that such creatures would swiftly become utterly dominant in the biosphere, sweeping all else aside. But this hasn't happened yet, although I believe there is an animal who delusionally believes that all its needs can be gotten for free from the environment, and that is just what that animal seems to be doing to the biosphere around it, so we have some anecdotal experiment evidence about how a second law violating animal might behave and how it might affect the biosphere. And yet, after all this time of life on Earth, all the creatures are using energy deriving processes altogether in keeping with the second law. Indeed the weird life (tube worms and the like) discovered in the last few decades around "volcanic smokers" deep in the ocean, almost poetically seem to be paying homage to Carnot's thought experiment, drawing work from heat and chemical potential blasting out of their central, hot life-giving "smoker" and casting the excess entropy out into the icy darkness surrounding their tiny thriving neighbourhood.
There are no biological perpetual motion machines of the second kind, and this is an extremely strong experimental null result. In particular, I believe it likely, given the experimental Szilard engine, that the Earth as an evolutionary computer (in the spirit of Douglas Adams) has likely "thought about" variations on the Szilard engine realised in molecular machines many times, so the null result is particularly pointed as a confirmation of Landauer's principle, a particularly pithy equivalent of the second law. An excellent paper showing exactly how the Szilard engine / Maxwell Daemon must heed the second law is Charles Bennett, "The Thermodynamics of Computing: A Review", Int. J. Theoretical Physics, 21, 12, 1982. Bennett used reversible mechanical gates ("billiard ball computers") to thought-experimentally study the Szilard Engine and to show that Landauer's Limit (the minimum amount of work needed for computation) arises not from the cost of finding out a system's state (as Szilard had assumed) but from the need to continually "forget" former states of the engine by casting the information-theoretic Shannon entropy of the sequence of gas particle states recorded by the Daemon out into the surrounding world encoded as increased complexity there.
Footnote: The following is not part of the answer so please don't read it as such but simply some results that come from the above line of thinking and which I would like to publish some time, so the following has not been peer reviewed (I'm just recording it here to establish priority since it is nowhere else on the internet). One of the ideas about nanotechnology that often bubbles to the surface in my mind is that there seems to be a lack of "big picture" thinking about how we might design nanotechnology. Thinking of the Earth as a computer in the spirit of Douglas Adams quickly shows, even by crude calculation, that evolution is way smarter than any group of designers is likely to be so that sythetic evolution by computer presents itself as a possibility. So what energy resources do we need to "Out-Doug the Earth?" (i.e. design complex nanosystems through synthetic evolution). One can use Landauer's principle to get some lower bounds that will apply even with reversible, e.g. quantum, computing as follows: the initialisation of each bit of storage needed even for reversible algorithms at the beginning calls for the expenditure of energy $k\,T\,\log 2$. Likewise, if a reversible algorithm's storage requirements grow throughout its running, its Landauer principle energy requirements are $k\,T\,\log 2$ for each bit of growth. We could imagine brute force search by some faroff in the future quantum computer if one could abstract the configuration space of all possible evolving biospheres to think of this gathering of possibilities as a colossal database. The memory storage initialisation Landauer limit energy needs of this databaseis likely to be greater than the total output of the Sun for a considerable fraction of if not all its lifetime so brute force would seem to be out. So let's think about a reversible synthetic evolution algorithm (indeed such reversible algorithms seem to exist in the literature) equivalent to the early biosphere. Estimates on the number of prokaryotes in the biosphere are of the order of $10^{31}$ organisms. With reasonable rough estimates of the combinatoricsarising in the asexual horizontal genetic transfer of these organisms and estimates of the frequency of this asexual transfer, we find we would need a "truly random" sequence input to our genetic algorithm to simulate genetic mixing at the rate $R$ of roughly $10^{29}$ to $10^{30}$ bits per second merely to keep abreast of the Earth's evolution. Sexuality in eukaryotes means that the bits per organism are much higher, but there are many fewer of them in the biosphere so that they too would require a random sequence of about the same rate as the set of all prokaryotes on the Earth: the basic sexual and asexual lifeforms are thus searching the configuration space at roughly the same rate, which is reasonable: if two organism classes in the same ecological niche (e.g. producer eukaryotes and prohayotes) searched the configuration space at greatly different rates, one would evolve much faster than the other and out-compete it. Now, if the input random sequence is truly random, a reversible algorithm taking this sequence as an input must grow in storage at at least this rate, so our basic, reversible genetic algorithm Landauer limit is $R\,k\,T\,\log 2$. So suppose we want to simulate the Cambrian explosion (10 million years) in 100 years for the good of our great grandchildren. We get $10^5\,R\,k\,T\,\log 2$ watts as our Landauer limit power requirements, or about $3\times10^{15}$ watts or about 30 grams per second: about a thirtieth of the total solar power lighting the Earth and roughly three orders of magnitude greater than the current human rate of energy consumption. And this is the Landauer limit. So can we use a lower $T$? Not with any benefit on Earth: the second law shows that refigeration will only worsen this result. So the natural place to do this computation is on a dwarf planet sized computer in the Oort cloud and possibly gather and solar energy by a near-Sun collector and beam energy to it. Even so, with reasonable estimates of how big the dissipation surface area would need to be to keep it cool. I calculate a few tens of kelvin as its steady state temperature when in steady state radiant heat exchange with the cosmic background microwave radiation is reached.