Smokes247,
What quality setting are you using?
Are you using "high" or "medium"? Try changing the quality in the AMV Convert Tool to "medium" instead and see if that helps during the conversion.
The "disk error" could also be in the way the original video you want to convert is encoded. Maybe it's not encoded correctly, or using a codec that isn't stable when used by the AMV Convert Tool? That might explain why you said some will convert 100% and some won't.
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