This is a bug of the Sound Blaster Pro. Here are some possible fixes:
Open the file "dosbox_albion.conf" with an editor and add the line "swapstereo=true" to the "[mixer]" category. (It should be under "prebuffer=80".)
I'm not sure if the included DOSBox version supports this feature, though.
Go here "http://www.vogons.org/viewtopic.php?t=16974
" and click "FULLY UPDATED ULTRASND FOLDER" to download Gravis Ultrasound drivers.
Unpack the folder "ULTRASNDPPL161" to the Albion folder and remane it to "ULTRASND".
Open the file "dosbox_albion.conf" with an editor and change "gus=false" to "gus=true".
Open "Launch Settings" from the Albion folder and change the digital audio driver to Gravis Ultrasound. You can also change the midi sound to Gravis Ultrasound, which is preferred by most people.
There also is a fan made Windows port of the game which not only doesn't have the stereo sound problem, but also contains additional bug fixes and 4x the original resolution in 3D areas. https://drive.google.com/file/d/0ByS3DU4n3Ke0Z0IydlpKdk11aFE/view?pli=1
Install instructions (even for the GOG version) are in the included readme file.
You can also get Gravis Ultrasound midi in that version, with this soundfont: http://sourceforge.net/projects/dooms-19-winx64/files/EAWPATs/eawpats12_full.tar.gz/download
Put the "eawpats" folder from it into the Albion folder.
Inside the folder is a winconfig folder which contains the file "timidity.cfg". Copy it into the Albion folder.
Open the copy of the file and change the line "dir c:\eawpats" to "dir .\eawpats".