The downhill running will do that to you. When you land, you are forcing the quads to contract suddenly while moving the joints in the opposite direction versus when they are usually working to propel you forward or uphill. The muscles get lots of little micro tears that hurt a lot for the next few days.
This will become a little less painful with downhill training, hence the reason for building it into your training program before trail races.
Thanks CO:) The massage therapist did good work on them and gave me some tips, like rolling and Epson salts baths. I figured it was from the downhills.
I call that kind of training "downhill pounding". There was a study showing that if you did it two weeks before a race with lots of downhill, your quads could handle that downhill better. It doesn't hurt to start earlier, of course, although I avoid it within two weeks of a race.
Super good advice from Bash!