I used ApplePi-Baker to install originally and I also use it to make and restore from all of my backups. I would be surprised if it is causing problems. It still sounds like you're having power issues, but if you have definitively ruled out that scenario, then you probably have a defective Pi. It could have even been damaged sometime after you bought it. Was their any extended period of time when you didn't use a case? Has it always been plugged into a surge protector?
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