I haven't managed to reproduce the exact same problem in a sample app but I have made it go wrong.
In the attached application I have a SplitContainerAdv which has other controls in it.
The top panel has a minimum size which fails to work when the application is run.
In my main app the layout of the SplitContainerAdv becomes confused after just closing the design window in the IDE and reopening it.
WindowsApplication411.zip