Hmmm. Thanks folks. Though the disparity in the number of clips doesn't lend a lot of confidence that the problem is related to clip library size.
My previous testing has been with a clip library of about 25 clips--and I've launched upwards of 10 instances of Sigil (both new instances and existing epubs) without getting this bug to rear its ugly head.
I'll try again with these provided INIs, though.
How do you have your GUIs arranged, by the way? Some screenshots of what widgets you have open and how/where they are docked/undocked might be helpful.