Concur, technique is off if you are hitting yourself in the head with your saddle. The book Skills Drills and Bellyaches has some great photos (and text) demonstrating the correct method.
The muscle issue gets better with time as your ride cross more.
Also-a tip from the Cyclesmart cross camp; if you shoulder your bike "across" your back rather than resting on your shoulder; doesn't hurt at all. Of course you take up more room since your bike is sort of sideways to the direction you're running. However, this has the added benefit of preventing people from sneaking by you.
I second the technique criticism. You want the top-tube of the bike to be resting on your shoulder with your right arm sticking through the main triangle. The right arm will then come under the down tube and reach up to grab the bottom of the left-side of the handlebars. The result is that your right arm will end up cradling the down tube of the bike - close to the head-tube (not close to the seat-tube). See: http://www.bicycling.com/sites/default/files/images/Cyclocross-Shou...
That being said, it is still quite painful for my 40+ year old self. My CAAD9 CX hurts less than my Lemond Poprad because it is lighter and the top-tube is wider. I also experience muscle pain in my right shoulder early in the season when I practice a lot, because lifting a bike over barriers and up to my shoulder is not a motion that I ever do outside of CX. Maybe I should do more weightlifting and Yoga in the off-season. I will say that I am tempted to find some of those early 80's women's shoulder pads that were the style in my moms wardrobe back then - because it is just uncomfortable for my tall, and bone-y shoulders.