okay ill admit, i'm not the most technologically savvy person in the world, which explains my lack of detail. However, I followed the youtube video for the "long" way to root my phone with mt FIRST thunderbolt, and it worked perfectly for ALL the ROMs i installed (both through clockworkmod recovery and rom manager) . My first thunderbolt's screen cracked, so I had to get a new one. I used the EXACT same method to achieve root with my SECOND thunderbolt, except this time I am having all of those issues.
I am wiping everything through clockworkmod recovery every time i try and install or re-install a ROM to get rid of those problems, but they keep on coming back. Like I said, i NEVER had problems with any ROMs on my first thunderbolt, and its really frustrating that i have no idea whats going on.