ScumCookie: I want to mention that for some reason, if you are using bMouse MIDI won't work no matter what you do. I don't understand why, I used to be able to do just this. When you mount .gog instead of .ins it will still play the CD music. If you remove the .ogg music files it just wont play anything at all. But as soon as you remove bmouse from the folder it will work.
I don't want to necrobump for no reason, I hope this information will be helpful to someone as it was a pain in my ass for over an hour.
-edit
Actually bMouse was never working at all. Spent all day trying to figure it out but found out I forgot to change Controller Type in the Settings executable to Keyboard + External, not Keyboard + Mouse. As for the MIDI issue I installed OUWB (wont let me link but its available on the forums) which allows you to switch between MIDI and CD through batch prompts which for some reason works just fine.
I can't replicate this. I downloaded & did a fresh install using latest Blood installer (setup_one_unit_whole_blood_2.0.0.21.exe), copied bmouse 0.6 into the Blood directory, and changed the dosboxBlood_single.conf thus:
[autoexec]
# Lines in this section will be run at startup.
@ECHO OFF
mount C ".."
c:
imgmount D game.gog -t iso
#imgmount D game.ins -t iso
cls
bmouse.exe launch blood.exe
#blood.exe
exit
Ran the "One Unit Whole Blood.lnk" from the desktop and the MIDI music started playing just fine.