I querried the Army Corp website for the Columbia, and noticed they had a sparse F.A.Q section. They addressed the Shad count discrepancies between Bonniville and The Dalles. I ask them to add a discussion of the Steelhead count discrepancies between the Dalles and John Day. I was promptly answered and I am pasting the reply below.

Hi Iwana, to answer your question the Army Corp of Engineers is aware of this discrepancy and actually did a study on it, we are trying to find an electronic copy of that to add to our FAQ page. The problem is caused by a combination of issues: John Day gets lots of adult fall backs (which means that the same fish could be counted multiple times as it moves up and down); there are probably steelhead holding in the pool between the dams and moving upstream later on; the configuration of dam could mean that more fish use the locks at The Dalles, though we have seen with shad that more go through the Bonneville locks than the Dalles. Obviously the count at the Dalles should be higher, but all the COE can do is count what goes by the window and report what they actually see and have no way of knowing how many go through the locks or are being counted for a second time.
In terms of the difference being Deschutes - yes the difference minus the tribal fishery (1,000 fish this year) should be about the number of fish going up tributaries.