I do not think I have every seen such a thing but that explains why it is not working they disabled it.
Have they considered that this might have been some random instance on there server. Is there any more information they gave you? what type of multiple instances where running open mysql connection? A bit more information would help but being how over 50000 customers run the software and I have never seen any issues like this I need more information as I do not really know anything software side that would help.