Yeah I have had big problems with this as well. my main issue is when I have a tempo change marker and a looped midi item which crosses it. If I remove or add time it screws everything up.
For example:
Create new project and set it to 120bpm
Insert an audio clip containing a drum recording that you know is at 120bpm
Insert a 90bpm drum clip next to it
Insert a tempo change marker set to 90bpm between the two clips
Make sure both clips are aligned to the grid
Now make a 4 bar midi click track, loop it, and drag it so that it extends across both audio clips and lines up so it syncs with both clips.
Now add or remove some time from the 120bpm portion of the project.
the midi click track is no longer synced with either of the audio clips. why?
Variable tempo is pretty much the main thing in Reaper
that should get a major overhaul as soon as possible.
The system is simply flawed and has too many bugs
to do any serious tempo work. I keep switching back
to Cubase or sometimes Ableton when tempo changes
are in question.