I mentioned this problem after I updated to 4.0.0. I just updated to the 4.0.1 and problem persists.
2 out of 4 songs I did as a test on 4.0.1 show BPM differences after recording just a couple tracks… The BPM is set by the BB and it has always been identical after a save until the 4.0 series of firmware. For example, the Aeros show 121 BPM after a save, while the BB still shows 120 BPM. This does not happen all the time. This BPM difference somehow introduces a gap at the loop Begin/End transition that will not record, causing a noticeable “dead air” gap in the sound output.
I use 6x6 mode in stereo exclusively.
I tried reverting to 3.5.1 and the problem goes away, allowing several dozen new song recordings with no errors, so it seems to be 4.0 related.