This can be closed Shippo has replied and it was a Shippo issue. Apparently they added a global CP account to users so i had two accounts active, one didn't allow the discounts but my personal one did. I'll let them explain:
"The error you received, 'eBay orders are not eligible for Shippo's Canada Post account', happened because of the fact that you currently have two Canada Post accounts active in your Shippo account right now, but they can only be used for certain orders. I'll explain more now.
So, the reason you received this error is simply because you were trying to buy a label from Shippo's Canada Post account, rather than your own Canada Post account, but that is not allowed, since eBay orders must be fulfilled using your own, personal Canada Post account, not Shippo's.
If you would like to deactivate Shippo's Canada Post account so that you do not see their rates and there is no confusion, you can simply turn it off in your Carriers Page by flipping the switch on the right.