I had the same issue: some of my PAL Gamecube games did not work on my Wii (region changed from PAL to NTSC). What is weird about my case: they stopped working for seemingly random reasons. E.g., I got an NTSC copy of Super Smash Bros. Melee (SSBM), because my PAL version did was not working. The NTSC copy did work. Yesterday I installed my PAL copy of SSBM and it worked, but only from HDD. That had been the same with Zelda - the Windwaker (PAL). Then I downloaded the cover art with the built-in function of USB-Loader GX. Then SSBM (PAL) stopped working. Even more obscure: the NTSC version had ceased to work, too. I deleted SSBM (PAL) and re-ripped it the same way as before. Now it works again, even with the cover art re-installed.
I did nothing to my CIOSs of any other shenanigans yesterday nor today.
I had a similar experience with Mariokart Double Dash. But in contrast to SSBM, which refused to launch at all (black screen after Nintendont), Mariokart showed the rotating Nintendo logo with Mario's voice before freezing. Here, I simply re-ripped the game. It is working ever since. I can even apply progressive patch and force widescreen without problems.
The most likely reason I can think of is that I had copied the Gamecube games from an older HDD to my current Wii HDD, which is the same size, but only 2,5". Even so, the image files should not be fragmented by copying all files in one big bulk. Plus, I never had the option in USB-Loader GX enabled to align installed GC games to 32k HDD sectors. And I always had "compress image" on.
Another hint is that I modded my friend's Wii and the same games did not work on his console, either. I had followed the recommended procedure for modding any Wii, without doing the same CIOS shenanigans that I had done to my own Wiis years ago, like updating d2x to v10 (final) and waninkoko's CIOS 38 rev 17 in slot 249.