"And I don't do pickup only"

That's probably the difference then. 

If it's pick up ONLY  (which the OP's was)  the code has to be entered.

It's obviously nothing to do with the app,  as in this thread Bricks wrote:

Confirm Pick Up

Enter the buyer's 6 - digit code, located  in their confirmation  email

"This is the only option I have available to mark as picked up.  App is the same"

https://community.ebay.com.au/t5/Selling/Buyer-paid-cash-on-pickup-and-didn-t-receive-a-code/m-p/259...

That's my experience too.