You stated that it works if you disable the AWE, is that disabling everything that loads or just the Mixerset line. When you set the resources in Win98, they are supposed to also be saved to your ATOEXEC.BAT file (IIRC, don't have Win9x hande to look into it.) Some things you can check:
In Windows, check the settings in device manager, and make sure they all match what AUTOEXEC.BAT sets them too. Then, using windows if you have to, make sure that the settings in Blood+ also match. Then try to play the game while in DOS.
If it still fails, get back into setup (using windows if you have too,) and disable all music (MIDI,) and give it a try. Also, you could REM out the MIXERSET line in autoexec.bat so that the AWE redirect doesn't go into effect. The first would could pinpoint that MIDI is the issue, while the second to indicate it's the card or if it is something else.