Im not sure about what could be the problem, but i do want to thank you for the link. I always knew the second connector was on the motherboard, but never knew if it was functional or if there was a good way to use it. Ive thought about using a second internal antenna to see if it makes a difference, but long ago forgot all about it!
Anyway, as I stated before, I think flashing back to stock and testing is your best option. If it works, then try reflashing your rom clean. If it doesnt it may be hardware related.
It may or may not have anything to do with it, but on that video it showed them plugging/unplugging that antenna several times. I know from experience that those connectors are very fragile, so check to make sure yours hasnt been damaged somehow.