I have TS2010 build 44088.  When I go to Railyard and select the Favorites button only favorites display.  If I remove some of them by clicking the green dot they are removed from the display list.  If I exit TS2010 then restart it in Railyard, the traincars that I removed from the favorites list are still removed.  You're saying when you remove traincars from the favorites list, they come back the next time you start Trainz?
 
Bob Weber