I spend a good little while trying to fix this problem and found no information on someone else encountering it so I wanted to document it when I could.
PKHeX launches perfectly fine, however, if you go to file -> open, it immediately throws a fatal exception in the COM service.
This Error isn't specifically caused by PKHeX (although it might be possible to code it to handle the exception and even work around it) but with Windows Themes. If Windows Themes is disabled (In Windows 7, 8, and 10), or if High Contrast Mode is enabled, it will cause this error preventing you from loading any files in PKHeX.
I apologize if there is a more appropriate way to say this. Criticism welcome.