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 2025 (1128)
64 bit application
RealBand 2025 (5)
Windows 10 Pro 64-bit
Intel Core i7 4800MQ @ 2.70GHz
Haswell 22nm Technology
16.0GB Dual-Channel DDR3 @ 798MHz (11-11-11-28)