Cool, @pilkster. We test the exact same way - with low cost products. It's really the only way to verify the live pipeline.
I'm puzzled by your observation that some click-backs to the return URL are counted and others not.
One clarification - to your question about multiple stores - as long as the cart is correctly implemented (like WooCommerce) the order itself gets sent to PayPal with a dynamic return URL as well as the product / cost data. PayPal will use that dynamic return URL in almost all cases. So, you should be fine with multiple stores. The return URL in PayPal is a fallback in case one isn't passed in with the order.
Something else to verify is that the GA tracking is in fact showing up on your return URL page (view page source).
Another factor is that you might have to wait for up to 24 hours for the analytics data to be available in your dash. The real-time view works pretty well, but if you miss the hit with that, it might take a while for the page hits to actually show up.
Anyway, hope that all works out for you. If you want to compare notes in more detail feel free to contact us through our site. Take care!