Pretty sure that any non-ELC mission results in an offset back to the government. Just because it's a government mission doesn't exempt it from that treatment. If it's not part of the EELV buy, then ULA gives some money back. I wish I could offer sources, but I'm not one to spend much time looking through public documentation to find it.
Here is a doc covering the GAO info on it.
http://www.gao.gov/assets/670/661333.txtFrom the doc,
"Prior to the December 2013 contract modification,
compensation amounts were loosely based on an average of 30 days of
launch pad use, and not based on actual costs. DOD and ULA negotiated
the compensation amounts annually, and DOD was reimbursed through
price reductions on ULA invoices submitted to DOD at the end of the
fiscal year. Under the new contract, compensation is based on some
actual costs, including factory support and direct labor hours, and is
approximately three times the dollar amount per-launch of
reimbursements under previous contracts. Additionally, DOD and ULA
plan to adjust the contract value at the outset of each fiscal year,
commensurately reducing the overall value by the number of non-DOD
launches ULA expects to sell in the upcoming fiscal year. "
However in the paragraph right above this, there was this gem as well.
"The new contract is also
expected to provide DOD with a better understanding of individual
launch costs than it had under previous contracts, as some costs are
now directly attributable to specific launches, such as propellants,
transportation, and costs associated with launch mission integration.
However, according to DOD, about 75 percent of the costs for cost-
reimbursement contract items are combined and not broken out by
individual launch costs, which may limit DOD's ability to identify the
cost of any given launch. "
NASA qualifies as a non DOD launch so there would be a reimbursement, but the amount reimbursed is hard to determine since so much if it is bundle together.