The Dalles dam traditionally sees its first 'fresh' steelhead start to show up May 1st. Take the steelhead count on The Dalles from 5/1 and John Day from 5/15. Many steelhead overwinter in The Dalles pool and finish the migration the next year. Those show up in counts from 1/1 to about 5/15. Remember they shut down counting from approx. Dec 1 to March 31 in all projects except Bonn anf LWG.
If you are already pulling annual counts for this time frame it comes down to the entirely unreliable count numbers at John Day. For several years they are way off to what seem realistic from using The Dalles compared to McNary. As you have found out more often than not more fish are counted at John Day than what is reported going over The Dalles. Those fish never seem to make it over McNary.