Even with the new version of Compressor I wouldn't push over too many clips past 30. I find if I keep each bath to around 30, Compressor works. So, load up 30 clips, apply your setting, and hit submit. Then wait for it to show up in Batch Monitor, then start another batch of 30, etc. It takes a little longer to setup this way, but yields less buggy results, in my opinion and experiences.
I should also add that you can make a droplet from any setting in Compressor and drop files on to it.