what version of premier are you using... cs4 and newer imports avchd natively, and i use it for .mts files from canon vivixia, i always thought, maybe wrong, that .mts and .m2ts were very similar... maybe they are or yes similar, but enough to throw things off, which in encoding i understand it does or doesn't. i am interested, and if you are cs3 or earlier, no prob im not advocating upgrade, i encourage the free transcoding route. best of luck.
i can't guide at all, but im sure if you are doing the command line x264, maybe take a peak at ffmpeg, but more specifically if you could run ffmbc. its a guy trying to use the guts of ffmpeg for bc, broadcast specs, avid, final cut premier compatibility. depending on your skills, that may be another avenue to explore,