What is the initial laser power? It would be helpful to know what percentage the fluctuation represents.
Also, What is the wavelength and line width of the laser? You might be seeing interference effects and as the relative length of the fibers change due to temperature/etc you'll get a change in interference.
Comment by Jimski: It was indeed the interference inside the second coupler caused by microphonic effect. To determine this, I connected only one leg of the couplers (as pictured below) measured the power using a photoamplifier and an oscilloscope, and the power was stable, other than some minor microphonic effects. But when both legs were connected the power began to fluctuate and the fluctuation could be excited to a large degree by tapping into the optical table. Looks like the microphonic effect was strong enough to alter the polarization and/or cause a phase shift and this in turn caused fluctuations in the intensity of the interference.
---------------------------
Laser -----| |----- Power Meter
--- Disconnected Leg ----
Additionally, the fluctuations which were initially observed one to two times per second were recorded using an optical power meter which was to slow to show real time microphonic fluctuations. However, when a photoamplifier and an oscilloscope were connected the microphonic effect could be observed in real time.
