I think Jason hit the nail on the head here when he said that if you restore certain options from a previous OS, your phone then might be trying to execute instructions that no longer are valid with a new OS.
I'm no expert by any means, but I have always done advanced restore after installing a new OS. I skip anything in the file list that refers to options or settings. I basically only restore address book, BBM contacts, and custom dictionary words. For my calendar, I do a sync with Outlook to restore that.
Going this route, I have so far never experienced the error messages or reboots that so many have. I also always start out a new OS on the default theme. Once settled in I might test themes for compatability.
Hope this helps.....
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