Just out of curiosity, is your recovery CWR touch? There has been word that CWR touch causes problems with some JB ROMs and I think I can attest to that as I was having bootloop issues once I tried a JB ROM. If you are using CWR Touch, I recommend you flash a regular version of it.
My phone bootlooped on me twice today and both with CWR Touch. I've since installed an older regular version of CWR and rebooted about 5 times with JD's JB v4 and had not one bootloop issue. For some reason I think there's a conflict between the CWR Touch recovery and probably the data of JB ROMs. I just got it fixed around 6:30pm and not a hiccup so far.
The last JB ROM I had on it with CWR Touch froze and bootlooped within 2 hours. So, so far so good.