MKV w\h264 -> When encoded in WMEnc9, stops after 1st pass...?

Hi there, used gdsmux to demux a rebuilt evo from a HD DVD containing the entire film (Encoded with h264 codec). So basically I've got an MKV with h264 in to be encoded... Install CoreAVC for decoding. Loaded the mkv into Windows Media Encoder 9 for encoding to VC1 for playback on my Xbox 360. However, after the 1st pass is complete on a 2pass encode, the program just stops and won't go onto the 2nd pass... Is there something I should do, that I shouldn't be? Or use a different decoder etc? Thanks in advance (The video is fully viewable, when you goto preview the input in WME9 you can see the video fine etc)

It does stop for a while; let it run, and eventually it'll start the second pass. I've found this happens on very long videos.

Ok I'll try that thanks, but I'm quite sure it has actually stopped completely....