I worked at a DOE site for over 20 years before retiring. During that time, I was involved with production, contracting and union issues at the site from both sides of the fence. Here are a few things to remember:
DOE uses an enormous amount of contractors (even in their own administration areas) as such, when gov. salaries were frozen, it was inevitable that it would overflow to contractors as well. My former boss at a small business set aside environmental remediation contractor billed DOE $350.00 an hour to run that job and brought in three cronies from his wife's company to assist him. He also got overtime. He ran the project in the ground and left with a bonus. What DOE contractor senior managers earn would make a good segment on "The fleecing of America".
DOE generally hates the unions, but can't touch them due to current CBA's. Former DOE Secretary Sam Bodman came after them on several issues and was beat down each and every time.
The DOE does not function as a branch of the federal government, they function as an autonomous entity and are basically out of control. They have become so large that they have no management continuity. DOE EM fights with DOE Nuclear who fights with DOE Science and Technonlogy,etc., etc.
I am not saying that the freezes are warranted, what I am saying is that I personally hired 200 hundred stimulus workers that never had any work to do. All at the mandate of DOE.