Emulator

Do you have dual core enabled?

It happens regardless of dual core enabled or disabled

It seems to regardless of settings entirely.

I've tried all the accurate settings too and I'm getting the same message.

Can you record a fifolog? The following process should hopefully capture it:

1. Ensure that on Config, under the Interface tab, "Show Debugging UI" is checked.
2. Check Options → Boot to Pause.
3. Start the game. A new black window should appear.
4. Select Tools → Fifo Player.
5. Set the number of frames to 30 (this may not be necessary).
6. Click "Record" in the FIFO player window.
7. Resume the game by clicking the play button in the main window.
8. Click "Save" in the FIFO player window.
9. Stop emulation.
10. Uncheck Boot to Pause.
11. In the FIFO player window, click "Load", and select the fifolog you saved before.
12. If everything went well, the same error message should appear, in which case you can close Dolphin.
13. You will probably need to compress the fifolog with 7-zip to fit it on the bug tracker.

The fifo recorder seems to behave a bit weirdly with "boot to pause", so there's a chance that this won't capture the needed information. If so, I'll try to come up with an alternative approach.

The same error messages did not reappear though.

I've tried recording a couple of times and the error messages do not reappear.

Unfortunately that one doesn't seem to have the needed info - I think the fifo recorder must lose the first frame (which contains the initialization stuff). What I should do is investigate what's going on there (and why the record button isn't consistently enabled), but instead, I've got a hacky workaround:

Try launching the game with the GameCube menu enabled. While the GameCube menu is fading to black, pause emulation, and then start recording with the FIFO player (again for 30 frames to hopefully catch the right part). This should ensure that the relevant information is captured (in addition to junk from the GameCube menu, but that's OK).

Thanks, that one does include helpful information. The problem starts on frame 8 and continues until frame 17 (you can see this by setting the start and end to frame 8, though you can't easily check the end point because looping in the fifoplayer re-uses registers from the start of frame 0).

On frame 8, object 0, at offset 0000437, they set both the CP and XF versions of MATINDEX_A to all 60. But then at offset 00000b6d, they set the CP version to all zeros, but don't change the XF version. On frame 17, object 1, they fix this by setting the XF and CP values to 60/0/0/0 (at offsets 0000023a and 0000026d).

Unfortunately I can't determine why the game is doing this without decompiling it. I think offset 000008da of object 0 on frame 8 is the end of GXInit (specifically __GXInitGX's call to GXSetGPMetric) so the stuff after that (which includes the change of the CP MATINDEX_A without changing the XF one) is game-specific. I can change the panic alert into a warning, though.