Can you alter the code so that these automated links are set apart from links made by the actual poster? Perhaps no underline, or a shade of the link that's different than normal links and closer to the default forum color for the user's theme.
Currently, it's annoying to try and parse whether the poster intends you to go to a link in his post, or it's an ad. If you refuse to separate the poster created links from the ad links, then that's the point where it becomes obtrusive. Instead, it should be a reasonable time saver to allow someone to quickly click an auto generated link if that post causes him to want to look something up, saves the small amount of time from googling.
Also, make sure that this software is also parsing shopping links posted by users, such as in the steals and deals, adding the GT reference code into them (and also stripping other referral code out). I noticed a while back that some posts on S&D and elsewhere don't have reference info added to the links automatically, and that's where you're more likely to get real sales and referral money.
No way to alter the code- it's injected via our CDN
And yes, it is parsing links already generated but only if they are links that are part of the affiliate group.