Stuart, I'll take a look at the unwanted custom command files. This isn't an area I've given much attention to, but I'll sort it out. Can I assume that it would be OK simply to not write those files when the event log option is used?
At present, what should happen with the auto-deletion of snapshots is that, if you use the Daily Folders option then the entire folder should be deleted, but if you don't use those folders then only .png files are deleted. The reason is that there may be other files of various kinds in the top level snapshots directory, and sorting out which files to delete and which to leave got rather complicated.
Now that there's another option of category folders it's become more complicated still. I need to give this some proper attention, but at the moment it's not high on the priority list.