running slow on ubuntu

[rainlake]

I've a amd 840 4 core cpu machine. I've windows 7 installed before. ps3mediaserver running fine.
after I switched to ubuntu (12.04 or 10.04), ps3mediaserver can not transcode well any more.
I figured out it looks like some pipe thing. I forgot how I figured that. but looks like that's the problem(i run mencoder on command line to transcode mkv to mpeg2, it's fast enough)
anyone has a solution for this issue?