The baseapplicabilityrules.xsd is related to the Windows Server Update Services. There are several XML schemas that are used for update metadata files. Some are used for all updates, while others are used for specific types of updates. Schema files can be found under the WSUS installation directory in the schema directory of the WSUS installation (typically C:\Program Files\Update Services\schema).
Although there is nothing we can do to correct this, here are some posts I found google searching.
You're probably correct that there is something wrong with Whatever's WSUS installation. However, I don't think that's an excuse for the Configuration Checker throwing an unhandled exception when it encounters a bad configuration.
I completely agree, I was able to break this on my setup and have escalated it to our developers. (forgot to mention that, sorry)
I'm sure we will have better error handling around this process in the next version of Patch for SCCM.