Sound goes out of sync after pausing video

Hi everyone,
Got a 1 month old Apple TV which is working just great with videos bought off the store... However I've run into a really annoying problem when watching videos that I've encoded myself. They will all play just fine, from beginning to end - unless I pause them. When the videos are un-paused the sound is badly out of sync, and no amount of pausing/unpausing stopping/starting will get it back in sync again. Best I can do is restart from the beginning and fast forward to the same spot and this usually results in a better sync - but not perfect. This happens with both SD and HD encoded video. They are playing off the internal drive having been synced over from my itunes library.
My Apple TV is on 3.0.1 firmware and I'm running iTunes on a Windows 7 laptop. I've been using "Any Video Converter Pro" (http://www.any-video-converter.com/products/for_video/)to re-encode my videos as I don't know much about the subject and it has an AppleTV option which makes it really easy...
Here's the settings used for a typical video file: 1280x720 resolution with a 3500kbs bit-rate at 25fps, audio bit-rate of 128kbs with a 44100 sample rate. 2 channels.
Would be grateful for any ideas on what's going wrong here as this is really spoiling my enjoyment of the apple tv.
Cheers,
Steve

Sounds like the encoder software causing issues.
When I encode on the Mac from my Camcorder to itunes/ATV I use HandBrake with good results - there is linux and Windoze versions versions available.
It has a preset for ATV as the destination which saves the hassle of tweaking the settings to start with....
It's been around sometime and was fantastic help when I went from Windoze to Mac a few years ago, and I wanted to re-encode all those files I had still in raw DV format from the camera.

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