Is it possible to keep CPU teams from going over the cap? I'm just three seasons in, and half of the league is already over the salary cap. I have the "Allow Extensions to Go Over Cap" box disabled, and the "Enforce Strict Cap Box" enabled, but just did a quick sim (5 seasons) with different variations, and in all of them, the vast majority of the league was well over the cap by the 5th season. I was hoping to play a career, and actually bought both the pro and college games together, but this is kind of ruining the experience and realism for me.

If they're going over the cap most likely it's not due to large signings (they should only be signing up to the cap and then signing min-level contracts to fill out rosters) but it could be draft picks are driving them over the cap. You can try lowering the min/max contract amounts for draft picks, or raising the cap for the whole league to see if it helps in giving them enough room to make decisions.

Any idea if this will be fixed in the newest iteration?

There isn't anything to fix.... there are scenarios, even with the hard cap, where the cpu will go over to sign rosters to 53 men or fill specific positions. They shouldn't be going far over, and if you see significant violations of this you either need to increase the overall cap, or adjust the min/max salaries for the draft and for FA. Otherwise if we put in a hard rule that they can't sign players to fill out rosters you'll end up with invalid rosters and will be unable to sim.

Also make sure that you're checking in week 2 of the season so the teams have time to cut players to get back under cap. Sometimes looking at week 1 doesn't work because teams are still at 85 players and haven't gone through that process yet.