MATH CAMPBELL This will be a flaw in the Logitech drivers where I'd imagine they aren't mapping the mouse buttons properly at the time you map them. Since all this app does is change two prefs in the Dock.plist (which don't affect either Spaces, Dashboard or Expose) and then reboots the Dock (which will also restart Expose, Dashboard and Spaces), obviously the logitech drivers are't saving the mouse button mapping to the plist file, assuming that the dock hardly ever gets restarted.
Apologies for this, but there's not much I can do to stop Logitech not writing drivers properly; the app has to restart the dock to get it to reflect your changes.