The lean forward in running can irritate upper and lower backs if you're not used to it or if you're increasing hill mileage too quickly. And as Kimmyt said... if you're tight in your shoulders, scrunching up shoulder blades, holding the elbows high and out to the side... all of these will fatigue and irritate the upper back muscles.
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2007 Look Dura Ace
2010 Custom Tonic cross with discs, SRAM
2012 Moots YBB 2 x 10 Shimano XTR
2014 Soma B-Side SS