Tried to contact the base public affairs office (PAO) for further information but just got voicemail, and email went unanswered. (Note: The role of a PAO is not to provide information, but rather "to act as the voice of the commander," to quote an NCO in a PAO long ago. The job primarily consists of making the commander, the base and that branch of service look good, and a good PAO member can expect to be rewarded with promotions and favorable follow-on assignments. Telling the truth is not necessarily guaranteed, and in fact there could be outright deception from a PAO. Most inquiries about base railway systems will go unanswered, and your name may very well be entered in a DOD law enforcement database simply for asking very basic, non-classified, railfan questions. And it was this way long before 9-11. If someone receives useful information from a PAO, it is the exception, not the rule.)
While there are some base railway systems operated by contractors (for example, the utility rail employees at Fort Eustis are contractors from Northrup Grumman), the contract employees use military locomotives, not those belonging to their corporate employer. No examples of military locomotives at a base being replaced by contractor-owned and operated locomotives come to mind.
Unfortunately the trend has been, not to convert base railway systems to contract operation, but to close them. Here is a fine example: the closure of the base railway at Hill AFB, UT, in May 2011. (This does not include the Army's rail shop, a tenant activity on base.) See: http://www.hilltoptimes.com/gallery/final-run