Simulink scope changes value depending on simulation time
Well it certainly looks like the sample intervals are too large and unequal. It seems like the noise BW exceeds the Nyquist rate or something like that causing aliasing and changes in output data intervals over time.

The 1st simulation has intervals of 0.1 and 0.9s while 2nd is 0.4 and 0.6 s.
(0.3897 rounded to 0.4).

Both average 1.0 second for 2 consecutive intervals and both have the largest change after the shorter interval in the 1st but after the longer interval in the 2nd.

at the moment, there is insufficient detail to recommend any fix for your accelerometer data except the output data BW is much lower than the signal or noise BW.