When you say autofocus is ok, do you mean it autofocuses properly where the "tilted" point is or where the point "should" be? The AF points on my EOS 3 don't line-up exactly either, they are all a tiny bit to the right (which is most obvious at the centre point), based on the circular area of the screen.

This is due to the screen not being seated properly. By that, I mean that the screen is seated ok as far as manual focusing (manual focusing is affected by the distance between screen-mirror-viewfinder, autofocus is done on the mirror so the screen is irrelevant) is concerned but there is still a bit of give left/right, so you might want to try and reseat it.

I found the best way to do that is to turn the camera upside down, unlatch the screen holder so the screen can move around, then look through the viewfinder (camera still upside down otherwise the screen will fall off!) and tap the body lightly left/right/back/front until the screen is where you want it to be.