Ok, some test results:
1. BootMii boot2 -> Sneek+DI -> system menu -> DML => Wind Waker works
2. BootMii boot2 -> Sneek+DI -> system menu -> HBC -> system menu -> DML => Wind Waker does not work
3. system menu -> channel that uses IOS254(set in the tmd) -> Sneek+DI -> system menu -> DML => Wind Waker does not work
4. PriiLoader -> BootMii IOS -> Sneek+DI -> system menu -> DML -> Wind Waker does not work
looks like running a libogc program somewhere in your chain of programs breaks it