I made different tests, based on my own guess.
First, I made a 1-hour clip (2.4 GB). (This time I made it CBR, not VBR, but I don't think that is the problem.)
I cut three commercials out, and saved the media file. It was taking "forever," so I cancelled.
I reopened the file, using the same index file. I made NO cuts, just saved the media file. It took "forever."
I reopened the file, but forced Splitter to re-index. I made NO cuts and saved the media file. Again, "forever."
I then deleted the index file and reopened the MPEG. As it started to re-index, I cancelled. The index file disappeared. THEN I saved the media file (NO cuts).
This time it only took only 3 minutes to save all 2.4 GB!
I think, therefore, that the slowness is related to the index.
Another thing: Scanning through the file (right-arrow key) takes longer and longer - slows down - as you go further along in the video. Perhaps there's a memory leak -- or possibly the algorithm for scanning starts at the beginning every time.
I think there's a problem with the index.