Hmmm... did some re-testing, and I am able to reproduce it in X3c now, punching in two bars in the middle of a 4-bar loop. Each take is 172 samples later than the previous one - about 20 samples more than half my total latency.
Interestingly, if I enter that value as a Manual Offset, then all of the takes are 172 samples late, but the error is not cumulative. Oddly, though, I have to enter it as a
negative offset (i.e. decompensation) rather than the positive value you would expect would be needed to compensate for latency.
Definitely an issue here, in any case. Apologies to the OP for not double-checking.