According to the wiki MMC6 is just an MMC3 with extra registers for RAM protect, but is there anything else I could be missing?
EDIT: Nevermind, just found this on the wiki:
Code:
Because write protection is generally only used to guard against corruption during power off, many implementations of iNES Mapper 004 simply omit the write protection. Leaving PRG-RAM always write-enabled removes most of the incompatibility between MMC3 and MMC6, and is sufficient to support the popular MMC6 games StarTropics and StarTropics II.
Removed the MMC3 ram protection bit and it fixed the no audio output. Just had to re-read the wiki a again!