Hi Jarrod,
It sounds like a field issue.
I know Encore has a problem with the “Automatic” transcode setting when using PAL footage – it reverses the fields causing the problems you describe. Are you using PAL or NTSC?
Try creating your own preset (based on one of the existing NTSC or PAL presets) and make sure the field order setting is correct.
I hope this helps?
Regards,
Tim