This is a big problem. I think there are two main reasons for this, and it has to do either with a lack of understanding how defense is played, or its just some sort of programming issue (inability to have if a-do b, if c-do d). Underneath zone defenders should always be involved first and foremost with stopping the run. LB's should not back up on the snap, instead they shoud step towards their gap and then confirm their key.
The other reason is that there is no ability whatsoever to use a 1/4 field safety. The quarters safety should actually be responsible for forcing the run and should thus play flat-footed at the snap, reacting to the release of the TE or the pad level of the Tackle, but in the game, the safety retreats no matter what, thus slowing down his involvement in the run fit.