Help exporting media

Hi guys, hope u can help
I'm using Adobe CS6 with a Matrox mini MAX. I need to export the media for a blu-ray & a DVD. The problem I have is that I captured the event with a canon 5d mkii (full HD) and a sony camcorder (1440 x 1080).
When I export the media then author it in encore the final piece seems to skip ever so slightly. As I'm charging this customer I need this to be perfect.
When selecting Mpeg2 Adobe asks me to select a preset, I don't know which one is the best to select so both will work fine.
Please help!!!!

Hi John
Thank you for the prompt reply,
When exporting the camcorder footage (1440x1080) for dvd its all fine but when I export the DSLR footage (Full HD) the movie skips ever so slightly but I'm afraid the customer may notice this.
Also something to take in to consideration is that the FPS are different on the dslr and the camcorder.

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