Results of two equivalent scenarios in SR This is not a homework question. It may appear as noob to most of you but SR is not my area of expertise and hence it seems very complex to me.

Question: Consider that there are two in-line pin hole separated by some distance. Both the pinholes at rest w.r.t to each other. There is a light source that moves relative to the pinholes. The relative movement is normal to line joining the pinholes. 

Case 1: I consider that pinholes is the rest frame and light source as moving. 
In this configuration when the light source and one of the pinholes are 
overlapping, a pulse of light can pass through the first pinhole and strike the other pinhole, passing it too.
Case 2: Now I consider pinholes to be moving and light source to be rest frame. From the rest frame of light source, I see that a pulse of light passes through the first pinhole during the overlap. This light pulse will travel to other pinhole but will not be able to pass the second pinhole because the pinhole has already moved. (For this to happen, I will assume suitable relative velocity and separation between the pinholes so that the second pinhole has moved enough to avoid avoid the light ray)
So, you see that although these two are equivalent scenarios, their result is not same. Now I believe that I might be wrong because the relative motion and light are normal to each other and hence it does not qualify to be equivalent scenarios and so their results are not bound to be same. Is my thinking correct? Or is there any other explanation or am I missing something important here?
 A: It is important to consider whether the source emits dispersed light or directed ray.
These examples can be considered either as the Transverse Doppler Effect or the or longitudinal Relativistic Doppler Effect (to be exact - a mix of longitudinal and transverse components).
The first example is the Transverse Doppler effect.
If the source emits diffused light, photon will pass through both holes in both cases. It's not a problem, and the photon will be red shifted after passing through second pinhole. Please note that if a photon approached observer at right angle it was released at oblique angle in source's frame.
If the source is laser pointer, the laser pointer has to be tilted backward to direction of motion. The angle depends on relative velocity of the source and can be calculated employing relativistic aberration formula. Otherwise a photon will not go through the both pinholes. Neither in first nor in the second example. For example, if a laser pointer is directed at right angle to direction of it's motion, photon will not go through the holes.
But, if laser pointer is tilted backward, the photon will pass through the both pinholes and it will be red shifted.
You can imagine a tube that connects pinholes.
Very simple animation in youtube. Maybe it helps to visualize.
https://www.youtube.com/watch?v=hnphFr2Iai4
https://www.youtube.com/watch?v=5-AAC4pemDI
A: Gaurav Goyal is right. The result of the experiment depends on which of the reference systems is defined as to be at rest. This can be shown in another similar experiment:
Two astronauts being in relative translational motion aim at a target with their laser guns. They hold their guns totally parallel. They each emit a short flash as they are flying by. Both laser flashes are moving in parallel and perpendicular to the relative motion of the astronauts. The target has the same vector of motion as the first astronaut.
If the first astronaut and the target is defined to be at rest, both flashes hit the target. In contrast, if the second astronaut is defined to be at rest, both flashes miss the target. Both reference systems are not equivalent, because the propagation of light is regarded to be independent of the motion of the source. Therefore the two postulates of SRT are in conflict and cannot both be true.
The experiment is explained in an youtube-video called Einstein's final prank.
Paul E.
