List of cases where GAO and Court of Federal Claims differ on the same legal question?

I do not know of any such comprehensive list.

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here's a short, incomplete list:

Post Hoc Extensions, GEO-Seis Helicopters

1 case, 2 different decisions

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There are several more such cases. The way to come up with a list would be to search COFC decisions for mention of the GAO, then go through each one to find out whether it was filed with the court following an unfavorable GAO decision, then see if the court differed with the GAO. To be safe you would also want to check periodicals like The Government Contractor. It would be at least three or four hours worth of work using a service like LEXIS or Westlaw.

While not directly on point, I would encourage you to take a look at Schaengold, Guiffre & Gill, Choice of Forum for Bid Protests, Briefing Papers No. 08-11 (Oct. 2008).

There were at least five cases in 2010 in which the COFC disagreed with the GAO. The most recent was Angelica Textile Services v. US, decided on October 26.