I had similar issues with my 660 until I worked out what was going on. In "Favourites" I had categories relating to each route/list I'd sent in Basecamp even though the routes were no longer on the 660. When I went into each category there was just one favourite left which had been common to every route; my home address. I clicked on the favourite and chose edit. In there was an option to choose which categories the favourite was shown in. Once I removed it from all those categories that pertained to old routes those categories disappeared from the list shown when I went back into the favourites menu option.
This may or may not be what you are referring to, but could be useful to someone else who needs to trim down their category list.
This may or may not be what you are referring to, but could be useful to someone else who needs to trim down their category list.
(I have to admit to OCD-like reaction when it comes to software applications not doing as I would wish / expect; I become like a dog with a bone) - maybe one day you will write and self-publish a fully edited "Basecamp & Nav V / Zumo 660 for Dummies"... (with sections specific to PC & Mac of course!) 
