Had this EXACT dilemma with my t4i after using extension tubes for macro photos but I have found a way to solve it. After resetting everything and updating firmware I had no luck. What you need to do is put a canon lens (or any auto aperture lens) on the camera, turn on live view and open the aperture to its lowest stop. Next, turn live view off, but keep the cameras power on. Remove the lens and replace with the manual lens you were having the issue with (mine was a Sigma 14mm 2.8). It should now be showing a correctly exposed live view during manual ISO. Hope this helps anyone with this problem.