Well then you're telling us right there that the video plays. So your N900 does support .mkv playback. Otherwise it wouldn't open at all.

Your video skipping is probably due to an encoded bit rate that is higher then your N900 is able to play back smoothly at the default CPU clock frequency. You could re-encode your video at a lower bit rate or try over clocking your N900 ( I know that video playback performance is mainly governed by the GPU, but it's worth a shot...)

The audio not playing is usually due to the audio in your .mkv container being encoded with some incompatible format like OGG Vorbis or something that you don't have the codec to play back on your N900. You could re-encode your video with standard mp3 audio or install OGG-Vorbis support to your N900.

EDIT: Just read this from the extras-decoders support troubleshooting page:
"None of the added formats are hardware-accelerated. This means that they need a lot of processing power from the CPU. Even though the CPU in the N900 is powerful, there are limits."

So I guess that over clocking your N900 could help quite a bit.