Marcia at a WebmasterWorld thread writes that Google Checkout is "washing affiliate links/tracking and not tracking those that are tracked with cookies, so that affiliates won't get paid for sales made by customers they send to merchants using Google Checkout." This is not a small thing at all.
Matt Cutts of Google replied to the thread after first spotting it at Threadwatch stating;
I posted this over on TW too, but wanted to make sure I said it here as well: I escalated this to the Google Checkout folks as soon as I heard about it, so I know they're looking to see if there's anything they can do pretty quickly to help on this issue.
So it appears it is not by design but an accidental by product of Google's most recent upgrade.
I assume more is to come with this major issue. There are enough speculation around Google hating affiliates, this just fuels that more.
Forum discussion at WebmasterWorld.