Just an update, for anyone that's been helpful and curious about this. 

I contacted ebay via chat again on a day that i was free, with a bit more assertive tone used. Nothing abusive, just reinforcing my frustration about it and pointing out something that dragged on for more than a month is unacceptable. The CS gave an assurance that it will be looked into and will contact me when it's resolved. 

After a week I tried listing again, and lo and behold it's now free. The free listing count also moved, with 3 being used and 37 left after a few autorenewals. I am also able to relist a couple of items, bringing total listing to 21 (42 items across all variations). I am unsure of the exact time/day it was fixed, as when i tried a few days ago the fee still showed up. 

So at this stage it seems to be an unexplained bug, and they seem to manage to resolve it but without any explanation so until now I am still unable to say for sure what exactly is the cause. Just want to say thanks to all that have tried helping me with this. Fingers crossed it doesnt come back again when October's monthly free listing starts.