The lag could be caused by poor buffer (if using VBR encoding) due to bitrate escalations. If you have a lot of RAM and a good processor, it shouldn't be an issue. If you're using overlay mixer (hardware acceleration), try turning it off. If using WMP, it'd be in the options somewhere. I forgot the exact button name, has Performance in it.
I know I love Quicktime with H.264 encoding, but apparently when it comes to Vista, Quicktime blows 10-12" of dick. No video will encode for me these days.