Here's the spectrum of the first 22 seconds of those samples, looking at the low frequency end of the frequency range :
This is intriguing. Firstly, neither spring constant nor damping appears to change much. Secondly, what is the resonant system at c 21Hz ? I've seen it before, and generally passed it off as the vertical compliance resonance. But in this case, it is such a long way from the c 8Hz resonance as to make one doubt...?
In any event, the primary change with 'break in' appears to mostly affect the system near 21Hz. But it does not change the resonance frequency, nor damping....simply amplitude.
The only effect I've seen remotely like it was when looking at a similar plot for playing wet. I wonder if it is somehow related to friction ?
But this doesn't look as simple as the suspension changes spring constant, or damping. It looks to me as though some other explanation is needed. Perhaps starting with an answer to what is the 21Hz resonant system ?
I haven't had the chance to listen critically yet, BTW, but would expect such difference in stability to be audible in various ways.