I believe Wiagara Video joiner also does batch converting. But you may need to buy it to utilize that function.
I know I've seen utilities that can help you.
Try searching majorgeeks.com.
DIKO. Check the "use DirectShow" option when you add video clips for any of the non-avi formats. Also, I highly recommend you do the "HC Encoder replacement" described here, as it increases the quality dramatically.
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