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I know that many people are against implementing Checkout for a number of reasons. The main reason that effects you guys is the tracking, but we have came up with a solution. Any customer with an affiliate cookie will not get the option to checkout with Google. Also I will try my hardest to keep any promotions involving Google Checkout hidden from affiliate customers.
This is the first I have heard of any such problem...
One particular shopping cart software will not record and pay commissions for sales made and paid via Google Checkout, and despite the merchant(s) requesting that the capability be implemented, it has NOT yet been done.
Unfortunately, this software is the default ecom offered by a VERY popular web host and despite attempts by one specific merchant to get tracking implemented for affiliate sales, the ecom software provider has yet to work a fix.