My 6 year old with DCD (and probably motor dysgraphia) had the same issue with the fluency scores, in that they were all a bit lower, but esp. writing fluency was lower at 80th percentile (everything else was above the 90th percentile). I think all of his reading scores were about the same with fluency being maybe 1 percentile lower. I don't understand why they call it reading fluency if it involves the child circling answers with a pencil. His CBM reading fluency was 130 wpm (weird considering how slow he speaks in normal conversations) which is 99th percentile. So I think the WJ reading fluency really doesn't have a strong relationship to other measures of reading fluency, like simply timing a child reading and counting the correct words per minute. His WJ reading fluency was a two or three percentiles lower compared to CBM.
Sorry about the scores not making DYS cut-offs but at least you have something to show the school. And it was cheap! DS's school actually did the WJ achievement themselves but they act like they couldn't care less about the scores. They basically disregarded the entire test.