[Wonder Warthog]

"Then again, if the Navy is the ‘preferred’ service for long term missions, why does the USAF run the X-37 long term missions?"

I suspect because the X-37 is unmanned. The relevant Navy experience doesn't apply.

[PIF]

Well, it is believed to be unmanned. However, the USAF is acquiring long duration space fight data, while the Navy sit idle (as far as we know) in that realm. The Navy only has sub experience which may be similar, but is far from an easy jump from underwater at any depth to space.