There is an option (or there was an option in 2013) on the Print menu to include the lead-in bar as part of the print. It's on the right hand side just below "Print Range" If you have notes in the lead-in bar BIAB will automatically print 5 bars on the first line and 4 thereafter. You can force BIAB to include this bar, even it is empty, by checking the box, but it's generally not necessary

Have you started your song in the lead-in bar, perhaps? If so, BIAB will print 5 bars on line 1 and then 4 bars, throwing off your expected alignment.

Normally a song starts in bar 1, but may have a couple of pick-up notes in the lead-in. (AKA the pick-up bar).

If this is so, just insert a bar in-front of bar 1, then copy the notes from the lead-in to this new bar and delete them out of the lead-in, and hopefully this will clear up your problem.

BIAB for Windows Version 2019 (643)
Windows 10 (1909)