I've played up to the second save point (in Narshe Caves), and MSU-1 playback on the SD2SNES is spotty. I'm playing on an SD2SNES with firmware 0.1.7p4, on an NTSC Model 1 SNES (I have an NTSC mini, and about eight different NTSC-J Super Famicom motherboard revisions I can test, though).
The opening theme never plays the .PCM version, and there seems to be some trouble particularly when switching from SFX tracks (such as the blowing wind in Narshe and on the intro precipice) and .PCM tracks.
To wit: Sometimes, battles will play the .PCM music, and sometimes they will play .SPC tracks. In addition, occasionally neither track will play and there will be either silence or a buzzing noise from the MSU-1 (which resolves itself whenever a new audio track loads, which in this instance is invariably a .PCM.
After the battle, the victory music always seems to be the .PCM, after which, upon returning to the field, the field music will play the .PCM reliably.
Loading a saved game produces NO music in the field until a new track is loaded, either by moving to a new area, or by entering a battle.
It's very difficult to debug on the SD2SNES (in addition, I am not the world's greatest coder), but what appears to be happening is that the "Play .PCM if found" routine is somehow taking too long to check if a .PCM is found, but not on a truly consistent basis. The game then defaults to .SPC. The buzzing is likely caused by confusion between switching back and forth between .SPC and .PCM files - I've seen it happen on occasion with other patches (MMX MSU-1, but it was fixed in the last revision).
I'm using a class 10 card with an average seek time of under .7ms, and a peak seek time of just a hair over 1ms, so I don't believe my SD card is the issue.