I looked at the source of the new loader and WiiGator changed some video mode stuff. To me it looks correctly, it looks at the region of the disc(4th caracter of the discID), and load the matching video mode. Before that it loads the menu with the video mode stored in your Wii and if it can't detect the region of the game, it doesn't change the video mode after the region detection. The old version always used the video mode stored in your Wii, that's why the same disc now causes trouble.
I see at least 2 possible reasons for this problem:
1. the disc itself has a PAL discID
2. the disc doesn't have a discID, but the loader detects it somehow as PAL, because at the place where the loader expects the discID, there's the wrong character(but's there's only a 1:50 chance that's identified as PAL then)