[curstpriest]

Are you trying 1 comic (folder) at a time, or like 10 comics at a time?

You may have to change your "save as gif" step in actions if you are trying to do multiple folders (lots of comics) or change/remove this step. I'm not 100% sure how all versions of PS batch handling works, you may have to read up on that, but it can handle it for sure =). I don't think this is the issue however.

Also, you may have to change output directory (DESTINATION) options in the batch job.

I assume it works fine when you just try to do a single folder? Make sure you are specifying a NEW directory, or else you will just get the new GIFs mixed in with the source jpeg directories, which is what it sounds like is happening.

I just got CS5 and haven't set up everything yet, I'll mess with it later.
Looks similar to old versions though. Looks like you can chose destination or save and close.
Worse case scenario, you should be able to use "Save and close" it will jam the gifs in with the jpegs, and then you can just do a search for *.jpeg, and delete them all when you are done, and everything should be in the right place (I know this is a backward way of doing things) and there is likely a better way to do it, but I'm not sure.