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There have been rumblings about sites with affiliate links not getting the best of treatment, but they're not all the same. Some are auto-generated, turning out thousands of pages at a clip and others are hand-rolled with individually hand-crafted pages. I can say that I've seen a couple of sites go down dramatically when affiliate links were added - yet others are still ranking well. It may be a difference in how the links are being done.
No idea at this point Allan, I hope someone can shed some light. I do know that people are being advised to "mask" the fact that there are affiliate links, and in fact I'm looking around for a redirection script myself - for more than one reason, to double check stats and have better info for myself on what's moving well.
That said, I don't think yours would be mistaken since a lot of regular ecom sites use their shopping cart on another server, even with another IP, and there's no ID number in your links.
A very simple and stupid error but when your creating dozens of web sites a week it takes its toll!
My best advice to you would be to stop looking at that toolbar. The toolbar is no longer a useful SEO tool in any manner (IMHO). Work on getting some good inbound links - get your appropriate directory listings, work on some one ways, do some reciprocals if needed.
Having affiliate links won't kill your site. Well, not in Google anyway ;). If it's a new domain, you need a strong link development strategy, good internal navigation (dire for a good crawl), good standard promotion outside of the free serps, continual fresh content being added and patience. I hate that last one, but that may just be me ;).
After several months it has only gotten the index page
Check the site programming, make sure there isn't a bug that might be triggered when a spider visits that you don't normally see, there are several spider emulators available, or you can just use firefox with the user agent switcher extension with googlebot useragent string set to active to do a rough check of your site programming.
For about a month I had the serps locked in for the error message googlebot received when it hit a site with such programming error : ), the only other time I've seen googlebot stop at the index page was due to reasons outside of what most people will have trouble with, hopefully that's not the case for you.