On my Onkyo pre-amp, stereo mode enables bass management, but direct mode disables bass management.
I was accidentally running in direct mode, and trying to figure out why my bass suddenly sucked. Pretty much the opposite experience you had.
I love using subs with music, once they are set up just right, which is tricky.
I tune the frequency response, time alignment, etc. on the sub to make bass on music as punchy and satisfying for music as I can, and leave it that way for both music and movies.