Yes, the issue with gain and loop sync was fixed in X3e. That doesn't mean there isn't still some issue with Battery, but the gain issue was not specific to Battery.
 
Is there a 64-bit version of Battery? I know a lot of old NI synths were never released as x64, and are therefore subject to the Bitbridge bug that could cause a loop sync drift.

Battery 3 has been x64 for a while now.  It has been and remains my drum module of choice.
 
Bob Bone

If anybody can repro the steps in my last post (repro'd with 64 bit battery and X3E) with another plugin please let me know.