Hi
SCS2006 will work perfectly well in native mode in both 2009 and 2010. In 2010 though it will only work up to and including build 44088. The multi player patch finally broke it.
If it isn't working in native mode for you it is most likely due to the route or rolling stock not being compatable with native mode that is causing the problem.
It doesn't work in 2012 at all, giving the same error message as the 2010 multiplayer version.
Regards
Brian