Most of these people you hear about loading short, or rotating magazines, stems from the maintenance, or improper maintenance of the M16 magazines in Vietnam.
Just like the rifle, magazines do need to be cleaned and cared for. The magazines could be disassembled as well. However, the spring in the mag had a proper orientation, but looked very similar forward or back. The spring's properties weren't right when oriented backwards.
A fully loaded mag with a backwards spring would not operate correctly. So, instead of checking every single mag to see if the spring was right (even then, you could analyze wrong), most people just started loading 2 short.
I've heard conflicting information about whether or not spring fatigue is a problem, either by constant loading, constant reloading, or neither.