GUI variables in memory

I am setting up a simple GUI using GUIDE. The GUI makes use of a class I have created, say Class1. In pretty standard manner, it populates 'handles' with instances of Class1 in the course of doing its thing.

Now my problem is the following: if I open, run, then close the GUI and subsequently modify Class1, then try to instanciate it (after mods) in the command line, I get the standard 'Class1 has been modified but instances are still in memory' warning.

However there is no trace of Class1 in the workspace. I can only guess that upon closing the GUI, instances of Class1 are not destroyed properly and still sit somewhere.

Anyone with the same problem ? Is there some explicit variable destroying to do before exiting a GUI ?