I can’t speak to your disappearing mts files, but I’m editing both mts & m2ts files with no problem (I switched from a Canon HDV tape camera to a Sony hard drive).
In terms of rendering, after weeks of pulling my hair out trying to use the Sony AVC codec running Vegas 8c and 9 under Vista 32 and even in desperation Windows 7, I switched to rendering with Main Concept and have nothing but smooth sailing. Not a single hiccup.
Ian Schwartz