Not sure why it happened, but I fixed it by deleting the stems, going File-->Open Special-->Open Using Stem Splitter-->Use Existing Audio Track, and the stems generated are in time with the rest of the song.


Band-in-a-Box® for Windows
Version 2026 (1224)
64-bit operating system, x64-based processor
RealBand 2026 (4)
Windows 11 Home
Intel(R) Core(TM) 5 120U (1.40 GHz)
12.0 GB (11.7 GB usable)