After upgrading to the latest version of spies.net, I noticed some problem points.
1. Spies threw an exception reading my old layoutinfo from my old project. This caused the rendering of the project treeview to fail.
NOTE: I had to remove this by hand from my project file.
2. I had an old non-existant assembly in my project list which I could not remove from the list using the spies GUI. Instead I had to edit and delete this assembly section from the project file from within a text editor.
NOTE: Spies would not obfuscate until I remove this entry
3. Its a pain in the arse, that the obfuscate options dialog location and size is not persisted. This means each time I open the assembly obfuscate option dialog I have to resize the dialog to see my full list of option and I have to scroll up/down.