It appears that they lobbied Senators Ted Stevens (R-AK) and Daniel Inouye (D-HI) to insert language allowing the services to veto joint bases decisions made by the commission.
Once again, it looks like the USAF’s real core competency is gaming the federal budget process.
According to the article, it looks like the USAF then used this language to blackmail the other services at joint bases more control and more of the budget.