tedster - 8:19 pm on Mar 21, 2013 (gmt 0)
I've been thinking about your question for a while. My first impression is that your -950 situation is not caused by a noindex situation alone - especially one designed to keep affiliate boilerplate out of the index. Something else must be contributing to your problem- usually something related to an attempt at keyword boosting.
That said, there is a difference between using robots.txt (the page doesn't even get crawled) and using a noindex meta tag (the page must be crawled for the noindex request to be seen.) I'm not sure if that clarifies the situation or not, but it seems to me it may be relevant for your analysis.