Is this a thing with some networks? Do they sometimes "not track" an upsell so they can make more off of you? I've noticed sometimes the upsell ratio is more off than it should be.
Yes. Split test networks. Sometimes, it's the offer owner who will scrub an entire affiliate network if a group of affiliates at that network provide low quality leads.
There's a lot of 'dodgy' networks out there. The key is finding the ones who don't engage in such activities.
Honesty is the best policy. If leads aren't backing out, it's better they tell you than scrub. Scrubbing gives a lot of networks license to print money. It's a bad practice.
A lot of networks - even big names - are notorious for scrubbing so I would also suggest to split test my traffic amongst 2, 3, 4 networks so you can compare performance between them
Hi bluecrayon,
Coincidently, I remember a thread from some time ago that is directly related to what you´ve brought up and thought it might be of interest.
Specially because it has quite a few recommendations and takes into consideration scrubbing: http://stmforum.com/forum/showthread...e-payout-bumps
Hope that gives you more insight 
Of course they do; they need to pay for fancy offices, 1st class air fare, lofts, hookers, blow and the tables at affiliate events. Not to mention, their nice cars and everything. Sorry but the supposed 10% cut affiliate networks supposed to make on offers; is not just "IT". Despite what they say.
I worked with a few networks; then went direct to advertisers.
Became friends with these advertisers.
Then for shits and giggles you know what they said? HEY why don't we look up how much _NETWORKNAMEGOESHERE_ shows as conversions total for period x to y , and lets see whats in my limelight.
And the difference was phenomenal. Some networks 'shaved' 5%, while others up to 20% of my leads. I didn't say anything though, because they will deny, call you stupid, come up with attacks and stupid high school drama. They simply lose my business, and I go direct.
Awesome post. As advertiser, I prefer to build relationships from the ground up and tell you about your upsell rates. Typically, I'd do this by communicating to you as often as possible. With that said, yes, Networks may scrub/shave conversions to pull the most profit out of the deal. It's all about the relationship that you have with your affiliate manager or client. Choose wisely my friend!
How do you guys go about getting in contact with the advertiser to work with them directly? I'd assume going to the offer site and looking for their contact details. Most of them only have a support contact email, and they never responded to my business inquiries, seems it's just for customer service.
Going makes sense in a lot of cases, but also doesnt in a lot of cases. There are a few big advantages of working with a network - of course i'm a bit biased but still -
1. Networks pay faster than advertisers. A good network will upfront the cash, pay you on a weekly basis and probably get paid on net30/60 or even later
2. Networks drive a lot of volume for one advertiser and hence get a premium rate. Unless you are a +10K a day affiliate, you probably won't get the premium rate (immediately)
3. Networks function as single point of contact + do the shitty work for you regarding setting up tracking, negotiating with advertiser for bigger budgets, new creatives, etc
4. Instead of spending a big amount of time doing all that stuff just to win 10-15% more than what you're making now, often its better to focus that time and attention on scaling your campaign, testing new ones, and optimizing ROI. Affiliates are good at driving traffic and that's where the focus should be on for them IMO as this will increase their ROI to the maximum