You've got a very unique issue here, one that's not easy to reproduce or figure out (on my end at least, since I can't reproduce it with the computers I have). I can't speak for other devs but I haven't had time to dig through your very long log file until now.
I did notice in your log that your game is in ciso format, which may be contributing to your problem. The ciso format can strip away "junk" data (in a lossy format) from the disc image that is used to pad the file to the full 4.7GB (wii) or 1.46GB (GC) to fit on the disc, which also puts data at specific spots on the disc (sometimes). Since Dolphin accurately emulates disc timing and reads of a GC/Wii, it could be a problem here.
What you'll want to check is if the game is a good dump, Right-click the game in Dolphin's list > Properties > Verify tab > Verify. If it says you have a bad dump, I suggest redumping the game from disc and verifying that the ISO is a good dump. Then if you want to compress the game to save space on your hard drive, use Dolphin's internal tools to compress to RVZ format (its a lossless compression).
If your ciso says it's a good dump, then we'll keep looking into other issues that might be causing this
I did notice in your log that your game is in ciso format, which may be contributing to your problem. The ciso format can strip away "junk" data (in a lossy format) from the disc image that is used to pad the file to the full 4.7GB (wii) or 1.46GB (GC) to fit on the disc, which also puts data at specific spots on the disc (sometimes). Since Dolphin accurately emulates disc timing and reads of a GC/Wii, it could be a problem here.
What you'll want to check is if the game is a good dump, Right-click the game in Dolphin's list > Properties > Verify tab > Verify. If it says you have a bad dump, I suggest redumping the game from disc and verifying that the ISO is a good dump. Then if you want to compress the game to save space on your hard drive, use Dolphin's internal tools to compress to RVZ format (its a lossless compression).
If your ciso says it's a good dump, then we'll keep looking into other issues that might be causing this