I reported the problem to AQA yesterday and was able to speak to someone in their IT department who was aware of the issue. Apparently "2 or 3 schools" have reported it to be an issue, and it does indeed appear to be a bug. They are having difficulty replicating the issue (as it only occurs occassionally and with no set pattern) and are not sure what is causing the problem. I was asked to contact them next time it happens so they can remote to the particular machine and find more about the fault.
Not much use really, but I suspect this is happening across quite a lot of schools but the issue has not been reported to AQA (I have had the issue for the past year and only just complained). All I can suggest is contact AQA so they will make it a higher profile issue.
And on a side note, I am certain that it is not down to hardware or software configuration, as I have had the same problem on a whole range of different workstations and laptops with different operating systems and flash player versions. It just appears to be either a bug in the Actionscript somewhere or just generally flash being unreliable (which it is).