If you update your firmware. after jailbreaking you will need to re-jailbreak. If you need to do this you go into iTunes and shift-restore then navigate to the firmware file you want to install.
You may need to put the phone in DFU mode so iTunes will recognize it.]
But before you go to drastic measures like restoring, you might want to try this:
http://www.modmyi.com/forums/pwnage/321011-unable-connect-itunes-after-winpwn.html#post2099891