Hasta La Motion!

I know this is more of a post-production kinda forum, but I thought someone here might be able to help anyway.

I was wondering if anyone could suggest how to get rid of flickering or strange waves of light or bars of colour that appear whenever I try filming projections.
We’re filming on a Canon 5D so its in progressive, and so far we’ve had the same problems whichever input we use on the digital projector. We’ve tried playing around with the shutter speed and with the refresh rate on the computer we’re playing the videos to be projected from but with limited success.
Can anyone help?!

Thanks,
Greg