Alright, I've corrected the issue. For posterity I'll post the fix.
You will have to modify the compatibility flags for your application directly in the registry (using regedit) as Windows' dialog grays out the checkboxes of x64 applications.
You can find all the application compaitibility flags at the following location in the registry: HKEY_CURRENT_USER\Software\Microsoft\Windows NT\CurrentVersion\AppCompatFlags\LayersIn that key, create a String entry with:
Name = The full path to the .exe of your application
Type = String (REG_SZ)
Data = HIGHDPIAWARE
This forces Windows to disable DPI scaling on the application, despite it being 64-bit. It corrected my fullscreen issue.
