I have a similar problem when adding files to my project:
the progress-bar is always on top, even if it has not the focus, and therefore hides part of the modal-dialog, that gets opened some lines later in the program.
It seems to happen because the progressbar gets initialized with the parent-pointer set to "NULL".
I have a fix for this problem on my working copy of C::B, that seems to work.
But on windows it works without this patch, so I think it's a problem of wxGTK or gtk itself handling modal dialogs.
I have seen your issue sometimes before, but it "works" not reliable.
Do you know which kind of dialogs are hidden behind the main window.
Are that normal dialogs (warnings, error messages) or only special kinds of dialogs (e.g. annoying dialogs, edit watch dialogs and so on) ?
(Annoying dialogs are the dialogs that have a "don't ask me again"-checkbox).
I found out some more. For example the "not found" message after an unsuccesful search has never the focus here originally. And as soon as I now accidently click on the workspace I have an modal dialog which is no longer visible. Not sure if that's what's happening every time, but a modal should imho never be in the background.
Where did you search ? In files or for files in the project or whatever search is possible ?
