Well don't forget about spiders. Unless you account for this a small number of clicks from many sources could be nothing more than a bot hitting your sites. Whereas with the larger volume a lessor percentage of hits are probably bots.
Next explanation. Probably shaving. Take 1,000 webmasters sending 2,000 clicks each a month with an average conversion of 1:1500. Now these webmasters are small time from the perspective of the program and the affiliate rep. The affiliate rep is under orders from the boss to somehow make up for the $50 PPS deal given to SUPER-BIG-FUCKING-WHALE-ILLEGAL-TUBE-OWNER who is sending 50 sales a day. They know they either pay the tube owner the $50 PPS or they will lose him. The rep is under a non-disclosure contract and is also told by the boss that since times are tough either they do this or the boss is going to have to lay them off. The rep has also been conditioned to hate the smaller affiliates (Never sending many joins, always hitting them up, pointing out bad ratios, arguing with them about things, not doing anything to make the boss praise the rep, etc). They are told that these guys sending 2,000 hits a month are just part webmasters looking for beer money anyway and it's their fault "for not working harder".
So the rep sets the shave for these 1,000 webmasters to 60%. This means that 60% of sales will not be credited to the affiliate.
Whale-tube-owner: 50 sales * $50 PPS * 365 days = $912,500 payout / year
(Would be $638,750 at $35 PPS)
Each of the small affiliates send 2,000 clicks a month at an average 1:1500 ratio but 60% is being shaved to make up for the payments to the whale. So:
1,000 * 2,000 * 12 = 24,000,000 clicks from small affiliates per year
24,000,000 / 1500 = 16,000 sales
16,000 * 35 PPS = $560,000 Payouts that should be paid.
However, the shave is set to 60%.
$560,000 * .4 = $224,000 actually paid to the 1,000 small affiliates.
$560,000 - $224,000 = $336,000 shaved from small affiliates per year.
And instead of seeing the actual 1:1500 ratio all these small affiliates see something like a 1:3500 ratio and are none the wiser.
Summary / TLDR :
1. Whale-Illegal-Tube-Owner gets his $50 PPS deal and keeps sending traffic.
2. 1,000 small affiliates get shaved at 60% rate and now have 1:3500 ratios (Real ratios: 1:1500).
3. Shaving of 1,000 small affiliates generates $336,000 per year to be used to pay the whale illegal tube site owner.
4. Program owner is happy and will have a drink with whale illegal tube site owner at the next show.
5. Affiliate rep keeps his job in a recession. Rep justifies it as being the small affiliate's fault and them getting what they deserve.
6. 1,000 small affiliates sending 2,000 clicks a month struggle and get screwed.
Laugh at me and deny it all you want and call me ridiculous (some will probably get angry) but I know somewhere there is at least someone sweating bricks. Let's not be naive.
Not everyone is dishonest but some are.