Yes, it's a limitation of mplayer. You can try a different build of mplayer to see if that helps, also you can try messing with the command line version to see what works on these m2ts for you. You can then add these options to your INI:
Code:
[MPLAYER]
PathToMplayer=D:\TVIX\Clown_BD BD Copier\Mplayer\Mplayer.exe
[COLOR="Red"]MplayerArgs=-zoom -framedrop -nosound -vo gl2 -loop 0[/COLOR]
WaitForMPlayerWindow=10