I tried that once and it failed so I restarted the phone tried at one more time and it failed again when it was testing to see if SU would work.Hmm...can you try opening Superuser and requesting the binary update a few times?
What I did to fix this issue was go in to CWM recovery then ran 3.07SU.zip that I downloaded when I first rooted my phone. When my phone booted up apps had SU permission.
Thanks for your ROM and time.