Dominant Frequency Peak Decreases with Increasing Window Size
Since your signal isn't sampled uniformly some strange things might happen when you apply FFT and look at the results.

What you should do is estimate the Uniform DFT of the Non Uniform Time Series.

One easy way to do it is use the reference code and analysis I posted on the question - Frequency Analysis of a Signal Without a Constant Sampling Frequency (Non Uniform Sampling in Time Domain).

Apply it on your data and things should behave more consistently.

One more thing, if you're after a peak, something which will make easier analyzing the data will be centering it. Namely make sure the samples have zero mean.