Above just based on the figures; reading the m file reveals a major problem -- you only processed the first N = 1024 points of the traces; the impulses aren't in the part of the signal you processed -- what you analyzed looks like
Again, however, even quiescent the two don't appear the same -- there looks to be a more-or-less cyclic disturbance on the upper (#1) as compared to the lower (#2). It's those frequencies your PSD uncovered because that's all the signal you analyzed by using nfft =1024.
If you look at the entire transient (which aren't all that similar in length, either, why? Are they actually sampled at the same rate or did just not run the second as long?)
Then, the results look much different, but the two still aren't the same at all--
There is, again, more structure in #1 than #2 as the time series would suggest; there's a pretty nice resonance around 200 Hz in #1 but a much broader spectrum of energies on #2. There's a little energy at the roughly 200 Hz location but more at what looks to be 2X that; then a whole broadband noise followed by another peak at 1550 Hz or thereabouts.
I would wonder if the accelerometer were mounted solidly on the latter, but something definitely isn't the same between the two.
The upshot is that you need to
- do what can to make the measurement conditions match;
- analyze the portions of the signal with the impulses
On the latter, I'd suggest probably should isolate those regions from the rest of the signal and process them separately and see how similar/dissimliar they are between each other as well.
Again, without knowing anything further, it's all just guesswork, but not analyzing the whole signal means you weren't looking at all at what you thought you were.
The rest is still something you'll have to try to unravel.