I work for a research institution funded by a DOE grant, not sure if that qualifies.
Technical decision-making is messy here. The folks making the decisions are academics whose expertise is in their research areas, not in software development. I will refrain from the horror stories. I have made suggestions for improvements to workflow, technology, etc. but they must always be routed through someone with at least a Master's degree. Usually it's easier to make the changes myself and hope for the best. It can be frustrating that no one cares, but OTOH there's very little pressure, as Bahamut noted. At this stage in my career it's not a great fit, but if I were <10 years from retirement, I might feel differently.
Part of the problem, I think, is that we're grant-funded. In a business setting, I can make the case for process improvements in terms of the bottom line. Here, it doesn't really matter if, for example, we have no bug tracker, because that doesn't really affect the grant-writing process that keeps our lights on.
Our research goal is to discover best practices for improving employment options for people with disabilities. Therefore, if I could change anything, I'd have my boss approach our software development efforts in the same spirit as the research, that is, with an eye to measuring more of it and implementing processes to improve those metrics.