I've just found that Prism & VideoPad work with AviSynth script files, I don't know if that would help - to force it to open the file in a particular way.
Having said that, I just opened this in VideoPad using this in an AVS file :
FFMpegSource2("00443.MTS",atrack=-1)
- and the preview (and Prism conversion too) was fine except that the colours were sort of negative-ish 
Brightness wasn't negative-ised, but red and blue were swapped around in a murky brownish world without green!
Can you not use VirtualDub to change the framerate in the Ctrl-R dialog?