Thanks Bob. A huge tip of the hat to you and the community's efforts to resolve this. Manipulation in the DAW is indeed the answer.

That said...
Recently I've been dragging the tracks I prepare in BIAB to Reaper. Just going with what works best from me, I've found two ways I am able to reproduce the misalignment shown in the OP's screen capture:

1) When dragging from the radio button in BIAB to the track in Reaper, if my Reaper play cursor is not at the very start of the track when I let go of the mouse, that track is not aligned with the others.

2) If I generate a track in BIAB, drag it to Reaper, then generate the next track at a slightly different tempo then drag that to Reaper, I'll get misaligned tracks. The tempos for each track have to be the same, and my tempo map in Reaper has to match from - start to end - how I have the tempos set for the whole song in BIAB.

Again, manipulating the tracks in the DAW is easy.

Bruce Hook - Soprano, Alto and Tenor Saxes
BIAB 2023 UltraPak | Intel i7 | Mackie ProFX10v3 Audio Interface | 1TB SSD | Reaper DAW
| Akai EWI 5000 | M-Audio Oxygen Pro 49