Strange Behaviour: Application Pseudofreezes

Hello out there,
recently I started to observe a strange behaviour in an application of mine:

The Programm is running without problem but if it is minimized to the taskbar or isn't in foreground anymore after some time the Application seems to freeze. This means that if you left click on the Task bar icon the UI isn't loaded completely as in an non responding program. But when you right click on the Task Bar Icon and then left click the UI is common into foreground immediatly.
Through debug writes I get the hint that every thread (even the background worker threads I have) in the application seems to stop until the combination of right and left click on the task bar icon is done.
I've got no idea what could cause such a behaviour. Does anyone here have an hint for me?
My application is written in c# on Visual Studio 2008 Prof. with .NET-Framework 3.5.

Thanks

Akademos

Are you running code inside something like a paint event that would not fire when the app is minimized?