Okay, that matches the other reports of issues from 5.0-619. Hopefully PR 4216 will be merged soon.
Were the Gecko codes really active when you booted through the system menu, though? Dolphin will only pick up on Gecko codes that are in (I believe) 00000000.ini, not ones you've set for Metroid Prime Trilogy.
It's still a mystery to me why this only started happening after you turned the ISO into a GCZ, but whatever, the PR fixes it anyway.
Were the Gecko codes really active when you booted through the system menu, though? Dolphin will only pick up on Gecko codes that are in (I believe) 00000000.ini, not ones you've set for Metroid Prime Trilogy.
It's still a mystery to me why this only started happening after you turned the ISO into a GCZ, but whatever, the PR fixes it anyway.