This is an issue that can occur with the Infusion kernel. There is an auto-root script that runs every time you boot your phone. There is a bug in the install script that will install the 2.3 version of superuser under some circumstances. I'm working on a fix for this and should have it available by the weekend.
For now, you can try flashing 3.07 as ppal provided in post #1681, or download from here:
If you get the old version again after a reboot, hang tight or use the Entropy DD kernel until the fix is available.