Was this the game that didn't have the usual filters? You disabled the GXSetFilter then?
It has GXSetCopyFilter inside files/PangyaRev.dol instead of sys/main.dol.
It seems ULGX automatically launches files/PangyaRev.dol anyway for some reason, so it turns out to be a bad test subject for testing games with multiple dols.
Metroid Prime Trilogy is a better test subject, because when you launch the game, ULGX launches rs5fe_p.dol. This appears to be the main menu program of the game where you select which game to play.
Then if you select Metroid Prime 1, the menu program launches rs5mp1_p.dol. It's at this point you lose ULGX dol patches, for the same reason you lose them when pressing HOME > Reset.
It seems ULGX can only patch a single dol and then launch it. If that dol happens to launch other dols, ULGX doesn't have some background thread waiting to intercept and patch them.
So ULGX deflicker paching for Metroid Prime Trilogy is not going to work -- we'd still have to manually patch all four dols in the game and rebuild the iso/wbfs with them:
rs5fe_p.dol (game's menu program)
rs5mp1_p.dol (metroid prime 1)
rs5mp2_p.dol (metroid prime 2)
rs5mp3_p.dol (metroid prime 3)
What you can do is tell ULGX to launch, say, rs5mp1_p.dol to launch Metroid Prime 1 directly, and patching will work, but then there doesn't seem to be a way to make it load your save game since that is handled from within rs5fe_p.dol.