I had this same problem on version 6 something. It took forever and several support tickets to get this working.
Edit your Synchronization Templates:
First change them to advanced view.
Under Configuration
select List Rules
change List Conditions QTY:* to more or equal and Quantity:* to 1.
Select Relist Rules
change Relist Conditions QTY:* to more or equal and Quantity:* to 1.
select Stop Rules
change Stop Conditions
Stop When Status Disabled:* to yes
Stop When Out Of Stock:* to Yes
Stop When QTY Is:* to Less or Equal
Quantity:* to 0
What the big deal is some times in Magento you can have a negative number like QTY: -2 and M2E Pro will list it as 2 in-stock, Also sometimes you have a QTY of 0, but still have in-stock set, so M2E Pro will list it as in stock. This is all on M2E Pro side, but I find Amazon does not always update in a timely manner. You need to lower you update frequency to longer then 15 minutes or the updates just stay in a state of update and never complete.I have mine set to every 30 min. Good Luck James Niland Niland Enterprise LLC