I just had this exact problem from another partition managing software. I did eventually find a solution after much hair pulling and digging through the registry while booted from alternate media. So, I'm leaving this for the next unlucky soul...
The software had modified HKLM\SYSTEM\ControlSet001\Control\Session Manager\BootExecute in the registry to run a program they had installed in system32.
Since I only had read only access to the registry, I renamed the offending program in system32, and then the system was able to boot. Then I was able to fix the key, which should be just "autocheck autochk *" in my case.