Tempo-map issues?


I’m attempting to create a track that features violin and guitar with virtual orchestra accompaniment. The form is:
- 28 bars of rubato
- 63 bars of tempo
- 5 bars of rallentando with a fermata on the last chord/bar.

The rubato is created by recording guitar and violin with the required interpretation; a tempo-map is created from this; the midi of the orchestra is added and sempte locked.
The Tempo section has rhythm section (bass, drums) created in Band in a Box and imported as both midi file (bass) and audio (drums - coz of the swing brushes - not available in Logic). For some reason the audio of the drums is not at the same tempo in Logic as it is in BiaB - so needs to be adjusted using flex time. Quantising in flex time is of no use in this instance - each beat needs to be dragged to the correct position.
The final rall is tempo-mapped from audio provided by Finale which contains the rall.

With each new step, what has been done previously is undone - e.g as the tempo-map for the rall is created, the tempo-map of the opening rubato re-aligns itself; or the sempte-locked midi-regions move (from a few ticks? to many bars). The Markers are also highly fragile and move around - a lot - even though locked to sempte. So far (over two months now) this has been going round-and-round - chasing my tail as I fix one aspect to find that another area has gone out of whack.

What’s going on? It seems I’ve been dropped into a ground-hog day time-warp.

Should I be able to achieve what I’m trying to do - it seems reasonable that I should - but so far it’s an ongoing failure - as if I’m trying to invent a light bulb.

Any thoughts or tips would be gratefully appreciated.