Well, it was actually a virgin install...
I just loaded an avisynth script. I added the video to the queue (avc-mp4). Then I tried to add the audio (ac3->FAAC) to the queue. But it complained that the input/output formats were incompatible. I altered some parameters and tried to queue it again, but had the same error. I tried again, but got the same error. I tried yet again, and finally it seemed to work. But then I noticed that although it had given me the incompatibility errors, it had actually added all those the jobs to the queue. That's why I deleted the duplicate jobs mentioned in my above post.
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