Thanks for the reply Ed:)

Stefan did some checks on the backend last week (see Incident #ACS00878 8/3 comment) and found that if there is a 301 redirect on an incoming URL with an adcode/affiliate code attached, the adcode/affiliate code does not get counted:

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 

Example

http://www.trossenrobotics.com/store/c/2662-Humanoids.aspx

which redirects to:

http://www.trossenrobotics.com/humanoid-robot-kit.aspx

So, if there are any affiliates (or adcodes) attached to the original URL, they are not being counted:

http://www.trossenrobotics.com/store/c/2662-Humanoids.aspx?af=suicidebots

because it redirects to:

http://www.trossenrobotics.com/humanoid-robot-kit.aspx

~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~

To sum up this thread, there are two major problems occuring:

1) Tracking is being disabled on all 301 redirected URL's containing ad/affiliate codes. 

2) No way to tell Search Engines to index correct URL (without code), which creates many duplicate entries, resulting in poor SEO ratings on the correct URL's and us paying $$ to affiliates who's links are being indexed by Search Engines.

 
Wouldn't it make more sense to have a cookie based code system, whereas anytime a user clicks on a URL with a code attached a cookie with that code gets placed on their machine before the 301 redirect happens, or something similar? That way, using regular expressions as you had mentioned, a 301 can be issued on individual ad/affiliate codes at a global level while still giving credit to proper ad/affiliate code.
 

I previously told all spiders/crawlers not to exclude all URL's containing ad/affiliate codes because I was afraid that we'll end up in "Google Hell" because of all the duplicate entry pages. That was obviously not a good idea, because we had many URL's containing ad/affiliate codes that showed up in the top 10 results, which is way higher than our own pages. Once search engines stopped indexing those URL's, our rankings obviously plummeted. So, I removed those exclusions. We're definitely in a catch 22 here because once the bots start indexing those URL's again, we're right back to the problem I mentioned above (#2).