Swapping the autoloaders would definitely help you isolate the problem.
I resolved a similar issue with mine just by disassembling the autoloader and thoroughly cleaning and reassembling. My issue occurred after trying to run PA-CF through the CFS (never again) the filament path was clear but the there was a lot of grind and dust in the auto loader.
Check out this youtube video below for a problem to look for in case you have stripped one of your gears.
