Thanks to our friends at the Center for Security Policy we now have a copy of the publicly releasable version of the Boeing protest.
Contrary to public option, Boeing contends that the competition was very close and the EADS won only because the Air Force misapplied the selection criteria and disregarded sections of the Request for Proposal.
Congress now has a decision to make will they try to nullify/not fund the contract now or wait for the GAO to hopefully rule in favor of Boeing.
It should be noted that a freeze was automatically made on the contract award under federal regulations due to the protest. But, those same rules gave the Air Force leeway to resume work in certain circumstances prior to the GAO ruling. The fact the Air Force is not fighting the freeze probably means they don't want to antagonize Congress again so soon. (Don't make them mad when next year's budget is currently being discussed.)
Our guess is given what Boeing says in their protest, Congress will make threats but will not move on the issue until the GAO rules on the dispute which could be in 3 months. (GAO has 100 days, June 19th, to make a ruling.)