I think I found the problem. I was not using the MP4 Unprocessed profile in the Conversion Task. Since I changed to it, things have sped up considerably.
I just checked on this and it appears to be working fine. If you save your EDL file along with your source video file with the same default (default suggestion by Custom Cuts) and then click Process with MCEBuddy it sends it to MCEBuddy to cut it and it picks up the EDL file ignoring Comskip.
Are you sure you aren’t confusing conversion with commercial detection?
If you want just cuts without any conversion you should be using one of the Unprocessed profiles like MP4 Unprocessed or TS Unprocessed
Like @RBoy said, attach your conversion logs so we can see what’s going on in your specific conversion
I just finished processing a 30 minute PBS show with the MP4 Unprocessed Profile. I created a cut at the beginning and one at the end. MCEBuddy took seven minutes to process the file.
Thanks for your help! The Unprocessed Profile made all the difference.