Well...I spoke a little too soon, After rebooting the phone the SuperUser problem returned.
I finally figured out a workaround, but it's not simple. The problem is caused by the fact that the Intercept Root application uses a trick to install the su application that involves moving it off of the main file system onto it's own tiny temporary file system. "Soft links" to this su program are then created in /system/bin and /system/xbin, but it looks like the SuperUser install/update process won't follow these links to install its own copy of su.
You can see more details on the underlying approach here if you are interested: joeykrim-SDX - Permanent Root for Epic (and Verizon Fascinate) - Confirmed
If you really want to use SuperUser on a stock Intercept that's been rooted using the Intercept Root app, I think you'll have to proceed as follows:
First, get a copy of the latest SuperUser su binary off of the SuperUser website and install it somewhere on the Intercept -- I'd rename it to something other than su. As of now, the latest version is at http://downloads.androidsu.com/superuser/su-bin-3.0.3-efgh-signed.zip
Then, remount /system in rw mode (I used Root Explorer) and edit the script /system/bin/joeykrim-root.sh and make 2 changes:
1) Increase the size of the tmpfs. It's currently set to 10K, but that's not big enough for the SuperUser version of the su program. Change it to 30K.
2) Change the line that copies the joeykrim's su binary (named "jk-su") to instead copy your new version of the SuperUser su program.
Now, every time you reboot the phone you'll get the SuperUser version of the su binary in the right place and SuperUser should work as normal. Of course, if a new version of the SuperUser su binary is released you'll have to update your copy by hand so that the joeykrim-root.sh script copies the new version onto the temporary file system it uses.
A fair amount of work, but SuperUser is working like a charm for me now.