This sounds a little strange to me. With the 7D (I imagine the 50D is the same???) the only thing that will make the shutter speed or apperature value flash is if you are in Av or Tv and the camera is out of range. Ie if you are trying to set the shutter at 1/800 while in Tv and the cameras metering says it needs a very large apperature that is bigger than it is able to open to the F4.0 (or whatever the maximum apperature is) will flash. Or similarly if you are shooting at a really bright light in Av with the apperature wide open, it will flash 1/8000 (or whatever the fastest shutter speed is) telling you that it even at this fast speed it thinks the shot will be overexposed.

The indicator for failed focus is a green dot on the right hand corner that flashes.

So that doesn't really answer your question, but that is the normal behaviour for the 7D and as far as I can remember the 450D I had previous.

I would think given the above it is probably more related to exposure than focus. One thing is flash, did you have any flash enabled because without high speen sync it wouldn't want to go over 1/250?

I'm not sure what else to suggest! Maybe post an image or two with EXIF that might help narrow down what it is doing?