Actually, it does behave exactly like a pendulum. The equations of motion are exactly the same. The issue, as Jasper pointed out, is damping. When you think of a "normal" pendulum, you are considering a lightly damped oscillator. The balloon, as I will prove below, is heavily damped.
For a damped harmonic oscillator (which a pendulum approaches for small deflections), the general equation is
$$m\ddot x + \mu \dot x + k\cdot x = 0$$
Where $x$ is displacement, $m$ is the mass, $\mu$ is the drag coefficient, and $k$ is the "spring" coefficient.
Sometimes this equation is rewritten as
$$\ddot x + 2 \zeta \omega_0 \dot x + \omega_0^2 x = 0$$
Where $\zeta$ is called the damping ratio, a dimensionless number. - more about that in a minute.
The solution to this equation depends on the degree of damping (the magnitude of $\zeta$). It is easy to see that
$$\omega_0 = \sqrt{\frac{k}{m}}$$
and
$$\zeta = \frac{\mu}{2m\omega_0} = \frac{\mu}{2\sqrt{m k}}$$
We solve this by using a trial solution:
$$x = A e^{\gamma t}\\
\gamma^2 + 2 \zeta \omega_0 \gamma + \omega_0^2=0$$
which is an equation with two (complex) roots:
$$\gamma = \frac{-2\zeta \omega_0\pm \sqrt{4 \zeta^2 \omega_0^2 - 4 \omega_0^2}}{2}\\
=\omega_0(-\zeta \pm \sqrt{\zeta^2-1})$$
When $\zeta \gt 1$ the roots are real, and the equation is that of an overdamped oscillator - meaning that it never oscillates, just slowly returns to the equilibrium position:
$$x(t) = A e^{\gamma_+ t} + B e^{\gamma_- t}$$
Where $\gamma_+$ and $\gamma_-$ are the two roots of the above equation.
All that remains is to prove that for a balloon, $\zeta \gt 1$.
Since a helium filled ballon is "lighter than air" we can put an upper boundary on the estimate of the mass from the mass of an equivalent body of air. For a 25 cm diameter sphere, the volume is approximately 8 liters, so the mass is < 8 gram (1 kg / cubic meter is a nice approximation of the density of air: it's a little higher, but we are estimating here).
Next, we note that a sphere moving through a medium has an apparent inertia that is its own inertia plus half the inertia of the displaced medium, so we add 4 grams for $m=12 \text{g}$ - except that since the balloon is lighter than air we will say it is $10\text{ g}$ and allow for a tension in the string of $2\text{ g} = 0.02\ N$ (we will assume massless string…)
The drag coefficient of a sphere in air is a function of the Reynolds number. If the sphere moves at 10 cm/s, we compute
$$R = \frac{D V \rho}{\mu}~2000$$
This means the coefficient of drag is 0.43, and the drag force given by
$$F = \frac12\rho v^2 A c_d$$
this is not linear with velocity, so we need to make a further approximation that the average velocity of the sphere during its motion is 5 cm/sec - then we can compute $\zeta$ as
$$\zeta = \frac12 \frac{\rho v A c_d}{2\sqrt{mk}}$$
Now we need to convert the effective buoyancy to a "spring constant", using the small angle approximation.
For a pendulum of length $l$ and (small) deflection $x$,
$$F = \frac{mgx}{l}\\
k = \frac{mg}{l}$$
In this case for a balloon on a 40 cm string with $0.02\ N$ of buoyancy, $k = \frac{0.02}{0.4} = 0.05 N/m$
This gives us
$$\zeta = \frac{1\cdot 0.05 \cdot 2000 \cdot 0.43}{4\cdot \sqrt{0.012 \cdot 0.05}}\approx400$$
So yes - $\zeta \gt 1$ which we set out to prove (quod erat demonstrandum). We conclude this is a heavily damped system, and the solution is a slow return to the equilibrium position without oscillation.
And that is your explanation.