For those who lost root but still have Voodoo and SuperUser...I had the same problem. I was running SafeStrap, so I had just restored to stock, uninstalled recovery, and then uninstall the SS app. I was, apparently, running an older version of SU, because when I updated the SU binaries , it was only to 3.0.3.2 or something. Anyway, I updated the binaries, ran Voodoo, and installed the JB OTA update.
From JB, SU reported that it didn't have root, so I went ahead and set up my account in the Play Store, updated the SU app, then went into SU and updated the binaries (this time it was something like 3.1.1). It said I had root, but root apps said they couldn't get it. I then went to Voodoo, temp unrooted, then restored root, rebooted and everything worked fine after that.
No idea if that will work for anyone else, but you may want to try a combination of temp unrooting (and then restoring root) with Voodoo, updating SU binaries, and rebooting after doing so. It might just need a certain sequence for you like it did for me.