Are you sure you have CS5 and not Premiere 5.5? (which is much older, and not a 64-bit program)
CS5 supports MP4, but not MKV...and 5.5 wouldn't support either.
Either way, it's a bad idea to edit with H.264 encoded footage unless you encoded it yourself using specific options.
You can re-encode small portions of your footage with a lossless codec such as utvideo/Lagarith/Huffyuv through virtualdub (though you'll need to write an avisynth script to get your file to load). I say small portions because lossless codec = hueg leik xbox files.
Another way is to use pwolf's avisynth plugin for CS5
. Takes more time to set up, but it means you aren't taking up space with lossless clips
Read ErMaC & AbsoluteDestiny's Friendly AMV Guides Lovingly Overhauled Largely by Zarxrax
. It goes over some avisynth basics, and how to use virtualdub (among other things). Also, the amvapp gives you avisynth, vdub and some other useful things including an avisynth plugin for premiere 5.5 - premiere pro CS4 which would be much less work to install than the CS5 one.