I had all kinds of problems with SuperUser after rooting and flashing a new ROM. In my case, doing a factory reset solved the problem.
The main issue I had was that, no matter what I tried, SuperUser wasn't remembering permissions.
I think I may have mistakenly upgraded through the Market, which doesn't work. I then tried flashing new version but never got it working properly so took a deep breath and did a factory reset - and of problem!
HTC One X+
Android version 4.1.1
Baseband version 3.1204.168.32
Kernel version 3.1.10-gf362097 root@abm032 #1 SMP PREEMPT
Build number 184.108.40.206 CL135278 release-keys
Browser version WebKit/534.30