No, not where they're installed but where they're registered. Open regedit and search on the name of one of your 64-bit DLLs. The tool gets the plugin list from the registry.
I'm thinking maybe it might be an issue with registry key mapping. Under 64-bit Windows, some registry keys are mapped so that they look like they're in the same place as their 32-bit predecessors but are actually in a different location. I ran into this problem with my product's installer when 64-bit O/Ss first came along - we used to use ODBC DSNs (we don't anymore, because of this) and when they were created using the ODBC Administrator applet they'd not be visible to my 32-bit interface. They'd be there if I looked with regedit, and appeared to be in the expected location, but it was a bit of deception by Windows because they were actually somewhere else and only mapped to the standard location.
That may be why I (running 32-bit Windows) can see the 64-bit plugins but someone running 64-bit Windows might not. If I can find where the real registry keys are, I can extend the tool so that it sees the 64-bit plugins as well. I'll need some assistance to test it, though, as I have no 64-bit O/Ss here.