ok ive solved it (well some bright spark on the media portal forum did lol) i just found the thread.
basically its actualy a bug in media portal and vsfilter, you just have to download a patch and place it into your media portal root folder.
theres the link for rc3 media portal
http://forum.team-mediaportal.com/at...itles-core.rar
once the file has been placed into the root folder, go into the ffdshow filters menu from the start bar and click "vsfilter configuration", now in the general tab make sure it is set to "do not load".
now go into the halli media splitter settings from the start tab then options and hit the + next to the compatability option then make sure "autoload vsfilter" is set to on.
your mkv files should now work perfectly, the reason it only affects some files is its a subtitle issue so any file without a subtitle should not have been affected.
all of these settings were only tested with ffdshow mind, not sure about other players ect, and halli media splitter ect needs to be installed, but if your using ffdshow it should be already.
the origional thread is here if any one wants to read a bit more indepth about the problem:
Pop-up error message generated for certain MKV files with UTF-8 subtitles - Page 2 - MediaPortal Forum
hope thats of help to you, my movies work fine now.