Install TS09 into a completely different folder.
I had three different Trainz (TRS2004, TRS2006 and TC1&2) all under the C:\Auran\ folder running fine but when I put TS09 in there, it didn't work. Then I found a message somewhere saying to install it sperate from other versions so it went into C:\TS2009\ all on its own, been fine ever since.