Sorry Digital-Ghost, it's not really as simple as ebay not charging it at all.  This is as simple as I can explain it.  For BAS we total up total of our sales that include GST (everything that we sell within Australia) and that gets divided 1/11th gives us the GST we collected. But GST-free sales and export sales are separate as they don't have GST of course.  Then we add up all the GST we paid on our purchases (which will include the ebay fees) and we take that amount away from the GST we have collected giving us a total of what we owe the Tax Office.

So by the time the end consumer buys a retail product they pay 10 percent GST total.  All the businesses along the way pay GST too but they claim the portion they paid back and essentially only pay GST on their added on margin at BAS time for want of a better term.

This is where I get confused, because if a GST registered business claims an exemption from ebay for the GST on the fees, how will that be accounted for at BAS time as you haven't paid for it on your 'purchases' etc but I cannot see that any business is actually exempt from being charged the GST on these fees now unless they are based overseas. 

Is the GST business registration only applicable to businesses not based in Australia but sell on eBay Australia?  That might be why we cannot register with an Australian ABN.  Just sayin....