I'm curious about this question...and I don't want to assume anything which is why I'm asking.
If you reprogrammed your video record button, did you do that for shooting stills to say something like FX/DX swap? Changing it in the custom controls setting, F2, for shooting stills would not change it's function when you've switched to Video mode. You'd have to go into the G2 setting to change it to something else that would only apply when you had the stills/video switch in video mode.
When shooting stills, I have the video record button set to select AF mode now...formerly FX/DX switch, but when shooting video, it still does it's original task, which I've never changed.