It is producing the Dolby Digital file but not the encoded .m2v file?

I am trying to encode as MPEG-2. I slightly modified DVDBest Quality 90 minutes and dragged my QT file and these settings to the batch window. I submitted a few clips successfully, however the last clip does not seem to want to generate a video clip, it just produces the Dolby Digital Professional 2.0 file. I tried this a few times with the same result.
Any ideas what might be wrong?

Depending on what version of OSX you're running, and how the data was transferred, you may be out of luck.
If you're running Lion, and your backups were made to a directly-connected external HD (ie, not a Time Capsule or other network location), you may be able to get Time Machine to "associate" the new disk with the old backups.  See #B6 in Time Machine - Troubleshooting, especially the pink box there.
If you're running Snow Leopard, you might be able to do a full system restore of your backups to the new HD.  See Time Machine - Frequently Asked Question #14 for detailed instructions.  That should leave a "trail" that Time Machine can follow to "associate" the new drive with the old backups.  Unfortunately, that doesn't always work, and there's no way to do it manually, as there is with Lion.

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