UPDATE:All fixed, I flashed back to stock, rerooted, and now everything works as it should!
I have no idea what's happening or why it's happening, but attempting to install a new ROM just goes horribly wrong.
Right now I'm running BB with Franco's Kernel M1. I tried doing a fresh install:
I wiped Data and Cache, then installed the Kernel, boot back into Android, first thing I get is the "Android is Updating" window, I let that finish, and now it skips over the first time initialization, weird. Next I notice it is incredibly laggy, I figure this was because of a fresh ROM. I look in Apps and it lists all the apps I had install previously are still there, wtf. It shows the grey android icon next to it, I have no idea why they're there. The Home button did nothing and there was no lock screen.
I guessed there was something wrong with BB, do I tried the same with AOKP, same results. Does anyone know why this is happening? Something is really wrong.