Interesting, thanks for confirming.
Pretty much every CMF file I have has the instruments change after pause/resume. Some testing reveals that it's only SBFMDRV v1.34 that is affected (either OPL version). It affects all Kiloblaster songs, Jill of the Jungle, Word Rescue, Math Rescue, Solar Winds, etc. Some of the most obvious are Jill's zeppelin.ddt, Kiloblaster's song_1.kb1 and Xargon's song_2.xr1. Even Jill's funky.ddt changes the percussion slightly. With Traffic Department 2192's td02.cmf, if you pause the song right at the start it only affects some instruments (not the main melody), whereas pausing/resuming after the main melody has started affects those instruments too. So it appears that this bug only affects instruments currently selected.
Since this is the only version of SBFMDRV I've had until I found your collection, it's quite weird for me to be able to pause and resume CMF files *without* having the instruments change!