Well, not having a sample of your code makes it hard to troubleshoot via crystal ball. The problem could be:
1. something related to your OS (Win7? WinXP? Win10?)
2. the compiler you use
2a. the framework you use to create the app (WinAPI, MFC, etc)
3. the version of the CC you invoke, this can be related to your OS version.
4. or something very particular to your system, unreproduceable on another.
You shouldn't change the Windows colors or themes when running your app. If you do make such a change you should probably force an entire repaint of the controls.
I've never seen something like what you describe, but then I don't change themes or Windows colors willy-nilly when I am running apps.
Creating an SSCCE (Short, Self Contained, Correct (Compilable), Example) would be beneficial.