I think part of the reason Dallas struggles with running the ball is that teams know when Dallas is going to run the ball, and to an even greater extent they know when Dallas is going to pass the ball. When Dallas is under center, they run the ball about 66% of the time. More recently (last 4 games) they've been above 70% and in the last 2 games they were 80% or greater.
When Dallas is in the shotgun, they're passing 85% of the time. The numbers are from Sturm's "Decoding Callahan" and a scramble is also considered a run so the true percentage of called passing plays from shotgun is going to be higher, if only by a little bit.
As Sturm pointed out Dallas is using shotgun 62.5% of the time, which is up from 54% last year and 44% in 2011. I've used his numbers and didn't include plays listed as "other" in terms of what package is used.
If teams simply played the run every time Dallas was under center and played the pass every time Dallas was in the shotgun, they'd successfully have the right defense called almost 80% of the time.