Preventing flicker when recording live presentations
The reason why this happen has to do with synchronization, or rather, lack there-of.

The projector displays its video-stream at one frame-rate and starting at one point, while your Canon records at a perhaps different frame-rate and starting when the projector image maybe has drawn part of the image.

The ideal approach is to use a common sync - in this case that is very unlikely to help in any case as the Canon don't have a sync input and the projector probably doesn't have one either.

To reduce the problem you need to make sure as a minimum that the Canon and the projector work on the same frame-rate. Ask someone or ask to look at the projector if possible. The start-point (for when the image lines start to draw) is worse - here you need to cross fingers and hope that when you turn on your camera that it will sync with the vertical blanking. As a rule of thumb: use 60i or 30p fps in America and Japan, 50i or 25p in Europe. However, some projectors can show at an internal rate rather than the one based on the electrical system.

Secondly, lower shutter-time (slower) and of course increase the f-stop (add ND filter if necessary). This will reduce the flicker but you can still get "bands" in the video. It will also be more sensitive to movement so here you need to balance/compromise. Too low and you get a strobo-effect instead.

Also try progressive record mode to see if that helps.

However, the best option in cases such as these is to ask for a copy of the presentation file so you can grab stills/video from that in post and super-impose those on the video, or cut to the presentation when editing.

Ask in advance so you can rig your camera in a better position to capture the presenter rather then the screen, but keep track of where in the presentation he is so you get the correct "slide" in post.