it sounds like you may have long exposure noise reduction turned on/auto, its a custom function that does a second exposure (black) the same shutter time as the 1st shot and will seem like its just hanging
set this to off and it will solve the problem or just wait for the same time as the first exposure, if its set to auto normally exposures over a few mins kick this function in
cant comment on 1 series but this is the case for the 5D, although with the 5D/7D i cant take more shots...actually i cant do anything so this is just a guess
for example take a 10 min shot...camera then takes a second shot (with shutter closed) for 10 mins then compares merges two images to reduce noise
I'm thinking the same. It was really confusing when you don't know what's happening.