Go to the MC and see if you have skipped searches; you probably do. If so, you have to make sure that you have enough SH horsepower to keep up with your acceleration demands. Also, if you just turned on acceleration, give it a day to get backfilled.
Also, make sure that the results from |from datamodel (which is a non-DM search that uses the constraints of the DM) are the same as the results from |datamodel and |tstats FROM. Also compare to a plain search. This will be revealing.