Any software used on government systems has to go through an accreditation process. This is to prevent you from pulling in some random code that may have security vulnerabilities or backdoors. Just because it is open source doesn't mean it is secure.
As an example, we've had to run security scans on jquery for god's sake and justify every occurence of random number generation to make sure it wasn't used for anything security related....
There are other things like warranty, support, size of the community, etc...
Overall, GSA is one of the best agencies when it comes to open source. It has definitely come a long way, but still a long way to go.