Sounds good about the stock, I just like to check everything to make sure something is not missed that could be an easy fix.
Thanks for your help on this and providing all this information it certainly does help and could lead to either a bug or at the very least a guide to setting up the plugins better.
Do you have the logging enabled for PayPal?
That might be something to enable if this issue continues to get more information on a transaction that has this happen.
It could be that some sites need to use PDT over IPN as the IPN connection is not working.
Let me know what you find out from the host or anything else.
I am making notes to update our setup guides about PDT to see if that helps.
Thanks