Hi Jason,
you should NEVER use the Bypass check if not advised by Microsoft Support.
The check is there for good reason.
If you install the fix on a System using the Bypass check you are actually installing dlls on a box which do not fix to the other dlls which are from an incompatible patch Level.
E.g. you will get the Problem if you have a System on RTM trying to install a fix from Post SP2.
If you now install the fix using the Bypass Setting you have a mix of RTM and Post-SP2 dlls on the box which cannot work together.
The check verifies if all components are on a compatible patch Level and prevent installing the fix.
Please open a Support case to get your System checked as I assume you have now an incompatible mix of DLLs on a box.
Cheers,
Stefan