Ok, good news ifI fixed my problem.

I reformatted my external drive, and that solved the whole problem. For some reason, it was limiting me

Now on to yours.

Um... how long does it hang?

I've not tried using the "batch encode"function, but I noticed that when I was encoding single files, it would hang at 99% for almost as long as the rest of the file took, and then all would be fine.

Are you doing separate jobs?

I think it only does one job at a time, but you can add as many files to a job as you want.