True to real life, if the QB doesn't have his WRs open, he'll check down. Against SMU with my lowly rated team and secondary, all their WRs had all the targets and catches because they could run free. But if you have a better team, you might need to make some adjustments. Either tinker with turning down HUM coverage (more open CPU WRs), up CPU pass block (more time for WRs to get open), or possibly the speed threshold (to allow more speed for WRs to get open).
This was one of my questions earlier, because the checkdown problem is one of my major ones I make sure I don't have, and I was able to avoid it on my set. The main changes there were HUM/CPU pass coverage 35, and threshold 25 (in which I once took a week playing with this slider, and determined 25 the sweet spot). Although in playing with this set, I'd keep the pass coverage still 95 for HUM but lower for CPU (as one of problems I had on my set was I was too good at passing, always top 5 in the country, but the upped pass coverage on this set has lowered that a lot.)
Also maybe a penalty slider thing like you mentioned earlier, as before I had always used Matt10's settings with my set, where the intentional grounding is at 99.