Quote - I believe it restores the stock customizations to maintain compatiblity with changes in the program. Otherwise you'd have legacy changes that no longer might work with a feature enhancment or fix.. and then you'd still have to do a complete wipe and reinstall.

The service packs don't do that. I suspect that the installer is just an updated full installer, which would write default preferences, largely for the reasons you pointed out. But, in this case, the download manager should have known I already had the program installed, and should have used the service pack instead of a full installer. At least, that is what seems correct to me. They do offer the SP on the web, and I did test to verify that it didn't overwrite the preferences and settings. 

Quote - When I enter an invalid serial number I think mine quits as well. Thats not a crash though, thats a program exiting and install because of user error with an incorrect serial number.

I'm not trying to be contrary, but if that is actually the correct behavior, they need to spend a little more time considering usability. If the serial number is invalid, why not pop up a box that says so before disappearing? Ideally, they would present you with the dialog to re-enter the serial number and a message indicating the one already entered is invalid. Then you could compare it with the correct one and fix it if there is a typo (hopefully no one is actually typing these things in anymore) or a copy/paste error. This is just standard practice in computing these days.

All in all, it's not a big deal. If you want to keep your settings, it's use SP that you can download from the website. It's much smaller anyway.