I followed the same procedure I do every time I install C::B on any machine, either that is Windows or GNU / Linux.
This time, on Debian testing 32-bit installed on VirtualBox, it produced a tiny black squarish pixel when I reduced wxPanel's border width to 0. When I resize it back to its original size, that is 5, it stays the same, but makes sizer visible around it. Also, notice the right menu that prevents me from previewing my GUI.
http://pasteboard.co/hKx07sW.pngSpecs:
Code::Blocks 13.12, 32-bit
wxGTK 2.8.12, wxGTK 3.0.0
P.S.: The problematic project uses wxGTK 3.0.0 for testing purposes if it helps a bit.