I tried Notepad and Notepad++ and both work fine:



I have the "Aero 7-11 Round" theme applied.
I know the theme works fine with apps that use parts of the Metro UI:

It seems like Start11Config.exe falls into the same category as ExplorerPatcher's properties window.
Unfortunately there is little we can do.
The dialog is a stock Windows one and if it fails to show it is probably a theme issue and you would need to seek support from the theme dev/patcher tool.
We have previously had an issue with folder picker dialogs with a tool which tried to change them to file open dialogs as it did it incorrectly.
The config is 32 bit if that makes a difference as your test apps are 64 bit.
If ExplorerPatcher is having trouble with a window too with the theme then that's more evidence there is an issue with the theme.