Just guessing here.... Maybe the HT standard has a deliberate bass boost in it? Wouldn't surprise me, given the wildly overblown bass in many theaters. If this is the case, the only solution I know of is the most recent REL subs which can be hooked up simultaneously for HT (5.1 LFE channel) and music (full range) with separate inputs.
The only other guess is that the "subwoofer" track has low-pass filtered noise, i.e., it simulates the LFE spectrum rather than a full-range signal. This might account for the level difference. If this is the case, though, one would think the disc would have high-pass filtered noise as well, to be used for setting the main/rear/center. Then you would be back to a level response again.
If all else fails, I'd set it where it sounds right on music and live with it for HT; this is a lot better than the alternative!
The only other guess is that the "subwoofer" track has low-pass filtered noise, i.e., it simulates the LFE spectrum rather than a full-range signal. This might account for the level difference. If this is the case, though, one would think the disc would have high-pass filtered noise as well, to be used for setting the main/rear/center. Then you would be back to a level response again.
If all else fails, I'd set it where it sounds right on music and live with it for HT; this is a lot better than the alternative!