If you like me to look at a waypoint or what have you and you're willing to post the file here I'll take a look at it.
I recommended v4.6.3 because it is so stable and I've tested it along with the all the others that came after it.
One suggestion I have since you have v4.6.3. would be to do another clean install and NOT import your existing data. Rather, try and recreate a subset of it and then attempt the same changes that have given you trouble. If the issue goes away I suspect maybe your original database is corrupted. In the past anytime I've experienced something like your describing with a database type program it usually is corrupted!
I'd be happy to post the files here, but I can't seem to figure out how? I'm now using 4.6.3 from a clean install.
I also re-entered over 300 points, one at a time. Took me 3 days :-(
If you did a clean install of v4.6.3 and then re-imported a corrupted set of data then it will now be corrupted too.
A clean install includes removing all remnants of the previous installation. Once that's done only enter maybe a dozen waypoints, a track and a route or two - something manageable. I suspect if your successful at the clean install and start fresh your problems will go away. If they don't then at least you're dealing with a small set of data for diagnostic purposes.
I reread your OP and you mention the issue both on a PC and Mac - that suggests to me your sharing info between them both - is that the case? I believe SUSSAMB has remained on v4.6.2 for Windows and I v4.6.3 for Mac as we both believe it's the most recent stable version - he may say different. I understand your frustration though!