I ran into this once. I find that making the patrol and just refitting constantly creates long load times. I always attempt to dock between missions. This greatly reduces load times. Another time it started doing this but I really never figured out why as I got bored with my present career and started over. The game returned back to short load times.
Oh yeah, I think you computer is not up to snuff J/K....
I had to throw that in there for some fun.
