two small junction issues

1 ive noticed that i am having junction levers disappering at which point i have to redue the track and add the default switch lever.
2 ive noticed that when i switch the direction of the locmotive when i go to give it throttle the game locks up at which point i have to save or control alt delete to restore it. and when i get back in the game puts me halfway across the map.

That sounds like data or program corruption of some sort.

Assuming it is data corruption (the second possibility is much more unpleasant) a simple first step would be to run a database repair - take the DBR steps shown at http://online.ts2009.com/mediaWiki/index.php/How_to_Perform_Database_Repairs and if that does not work then the more rigorous EDBR may be needed.