This does not have anything to do with type conflicts. You likely have two applications that are using the TestStand Engine. One is completing and modifying the StationGlobals.ini file. At the same time, your second application also is modifying the StationGlobals in a different way. If you save the second application, it will overwrite what the first application did. So you are prompted to decide which version you want to keep.
This dialog occurs because there is code that calls Engine.CommitGlobalsToDisk. This method has a parameter called "promptOnSaveConflicts" that gives the option to display this prompt. However, I believe this method is likely called internally by the ApplicationMgr control. I haven't found a way to have the ApplicationMgr call this function with a false parameter value. Before shutting down your application, you could call Engine.CommitGlobalsToDisk with the false parameter and then shut down, which should make the problem go away.
However, you do risk overwriting global data so I would examine what you are doing to see if you expect to have multiple applications modifying the globals. If this is unexpected, you likely have a problem. I didn't quite understand the different between your GUI and EXE or what you are trying to accomplish, so perhaps there is a better way to implement what you want to accomplish.
