One thing in RB that I've learned to watch for is the slider that is located in the mixer panel between the tracks and the AUX/Subgroups section. I think it is labeled 'ALL'.
If this changes it definitely affects the final volume.

The Default synth changing (as you mentioned) would also affect volume.
Selecting 'MS GS wave table synth' (instead of Forte) could affect the final output just as well, as settings inside the synth itself could be different.
Just a couple thoughts.
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