I had the same problem you having with Media Player. I finally gave up MP trying to make it work. My method involves a Freeware program "STOIK Video Converter"
http://www.stoik.com/downloads/downloads_frm.htm
I use the video convertor to convert to .wmv, also you have the option of video quality. I played with several video quality options, I created a different file, loaded it to a directory through Activesync, then played it on Media Palyer. Crude but effective....My little 300mhz Axim liked the "Video for e-mail and dual-channel ISDN (128 Kbps)" option