For me to get MOV files working under BS.Player, I have to install Haali Media Splitter and during installation enable AVI, MP4, OGG/OGM support and then install MPCVideoDec.ax.
Afther that it just works for some reason! :)
Quick-guide:
1) Install ffdshow, disable h264
2) Install MatroskaSplitter (with settings as stated above)
3) Install MPCVideoDec.ax and register it regsvr32 MPCVideoDec.ax
MPCVideoDec.ax can be downloaded here.