What music files are you using, and what version of the game? I have been testing the latest .cia on my 2DS and N3DS and they are both working, I thought that I had fixed it.
I'm using eduke32_musopl.zip from http://www.dukertcm.com/knowledge-base/downloads-rtcm/src-eduke32-patchs/. It does the same thing with the shareware grp included in the zip as the Atmoic Edition grp.
It appears the issue was with the format of the OGG files, or more accurately, the amount of channels. The files in that package were high-VBR 16bit 48kHz mono. I tried another package on the site containing 128~ VBR 16bit 44kHz stereo files and they worked fine. I re-encoded the mono files to stereo and the game is working now. Seems strange that mono files would cause an issue like this.