There are a couple ways I use to check devices for root.
Method 1:
Check that your phone is properly rooted with the "superuser" app's built in checker.
It should say what version of the su binary you have in '/system/xbin/su' or wherever.
For me it says:
su binary v3.0.3.2 (15)
-rwsr-sr-x root root /system/xbin/su
Method 2:
Now for the less obvious method. You can try using adb to shell it directly. Show me what the output of `whoami` is.
If you have a warning(s) about not being root in "superuser", something went wrong.
If something is wrong in adb's shell (i.e., you don't see `uid=0(root) gid=0(root) groups=0(root)`) then something is off with the rooting method you used entirely.
I had an update from Sprint that pretty much caused superuser to crash, and my root method to set my uid to `null` and make it impossible to run any root apps correctly. It took 4 hours to figure it out and write a patch.. Now it says `id=0(root), gid=0(root,system) groups=0(root,system)`.