Please excuse the necro, but I have the same problem. Header files' names are impossible to see with a dark background color in system settings. I figure it might be possible to get around this problem with a proper .gtkrc file, but I wouldn't know what options to put in it to make it affect header files' labels.
Edit: I'm using SVN r5499 under KDE.
Update: I fixed it by going into src/sdk/cbproject.cpp and on row 1053-ish, I commented out the below code and re-compiled. If we could get an option for this behavior in the settings dialog that would be preferable.
if (!compiles)
tree->SetItemTextColour(ret, wxSystemSettings::GetColour(wxSYS_COLOUR_GRAYTEXT));