Dialog MessageBox sometimes hidden behind the main form

Is it always the same message box (for the same message?) coming the same form?

Ideally, you should try to find some way to reproduce the problem at will, or at least automatically. This will make your debugging easier and you can then be sure that your future change will have fixed the bug, rather than have to wait for a few weeks for the feedback from your users.

If it is always the same message and in the same window, resulting from the same action, and if the MessageBox call is reasonably easy to trigger from an user point-of-view and if your UI is relatively standard, you could automate the UI with an AutoIT script and have it run in a loop until the problem happens.

And/or, you could create a "debug"-build of your applications that you could give it to some users (preferably the ones that seem to run into the problem the most often) that would write the contents of a StackFrame object to a log file or something similar everytime before calling a MessageBox (you could create a wrapper around the MessageBox to make this easier).

Then, when one of your users gets the problem, you can look at the log file and see where it came from (source code file, line, calls stack etc). You could also compare this to the logs from other users and see if, everytime, the MessageBox comes from the same location or if it varies. This would show you where the problematic MessageBox is called from and where.

There may be easier solutions (especially if your application has a lot of assemblies) involving some .Net debugger that you would attach to your application when the problem occurs in order to see the call stack, etc, but I only did this with native applications (using OllyDbg) so far and not .Net. Others may be able to expand further on this idea...

Some overloads of the MessageBox.Show() method take an IWin32Window parameter as the first argument. If you pass in your Form as that first argument it should prevent this from happening.