This has always been a problem with Adaptive Payments, just not always so severe. Paypal's Express Checkout product has the best solution to this in that a payment cannot be completed without an explicit API call by your application. This makes the payment confirmation IPN redundant.
It is a more complex integration, but our product has been much more stable since we made the transition to Express Checkout.
This does not however prevent other problems with IPN delivery on refunds and other post order activity. Paypal's IPN infrastructure is pretty weak in general, very poorly documented and completely untestable.
The issue here is that Express Checkout isn't available in all countries. When I was integrating PayPal for the startup I was working at last year we had to use Adaptive Payments because of this. I don't mean some small South American county nobody has heard of, the business was based in Ireland.
As other commenters pointed out we didn't have much choice of providers because of our business model (hotel booking). Stripe and Braintree didn't want anything to do with us, so we went with PayPal to start with. I think they are now using RBS WorldPay, but even that had it's issues...
It is a more complex integration, but our product has been much more stable since we made the transition to Express Checkout.
This does not however prevent other problems with IPN delivery on refunds and other post order activity. Paypal's IPN infrastructure is pretty weak in general, very poorly documented and completely untestable.