I used to get back pains say on a two hour ride on the flat, during the second hour I would feel it. The stronger I got the less that became, but it essentially went away with a fit and a new saddle. Now I just get sore when I do a lot of climbing, pain only when I climb and do too much so that I am tired and the body just cramps up. So I would assume that something about your fit/saddle is not 100% so that it puts your back muscles to more work than they should.