I have never had a problem with tracking and we have 100's of networks and merchants using our platform as well. But I HAVE been there and it is ONE of the MOST frustrating things about this business.
I'm so glad those days are behind me. We have a proprietary platform in house and 100's of networks and merchants private label it as well. I have had more than a 2% discrepancy in a LONG time.
I've never had a problem with Tradedoubler, AffiliateWindow and AffiliateFuture. They are all UK networks. The first 2 I mention are actually the biggest UK networks of the lot.