To exclude an application. Goto Windowblinds configuration windows -> Left panel -> Click "Per application" -> Right panel -> click "Add.." button. -> Navigate to that application directories. -> Highlight that application "xxx.exe" -> Click "Open" -> on "Per Application Settings" Windows -> Total exclusion -> Tick " Ignore this application and do not skin it"-> Click "OK" button.
and that should do it. Just make sure you select the correct .exe file.
On system colors, I really need to know how you did the setting. Is it via Windowblinds configuration by using its Modify style -> Change system colours button or via Skinstudios and modified colors.
Stardock Community Assistant.