I don't know what to tell you other than to maybe go down in difficulty.
I play on Heisman, and I don't have any of those problems running. I think running is quite smooth and well done. In the fourth year of my dynasty, I took an 89 OVR HB on Kentucky through the SEC grinder and still got 2,141 yards on 351 carries for 23 TDs. In the fifth year of my dynasty as Bama OC, my HB came in second in the Heisman by a measly 2 points.
Lots of questions arise though.
What type of playbook are you using? What type of running plays do you run? How often do you run? What kind of linemen do you play/recruit? What types of formations do you choose to run out of? Do you run option, out of the shotgun, single back or with a FB? Do you flip the run based on what the defense is showing you? Do you audible out of running plays when the need arises?
Personally, I find that running out of the shotgun or a single back set is much harder than running with a fullback. Try a pro-style offense. I run out of Western Michigan's playbook.
When you're running, you need to follow your lead blockers, and hold off on using the Sprint button until you need to make sepration, or hit a hole.
Be wary of always trying to bounce to the outside. Defenders in NCAA 14 are good in pursuit, and the winning strategy is usually to cut to the inside at the crucial moment. If you always try to bounce outside, you're gonna take a lot of losses.
Also, in a pro-style set, try to send the WR in motion away from your running play to drag the CB with him. No point in ruining a good run if your WR can't hold his block. If it's zone and the CB doesn't follow, bring him back. As a rule of thumb, if they're in zone like that, you absolutely want to cut inside because you will be outnumbered to the outside.
Try to use heavy power runs, but occasionally mix in a counter. When you're running the counter, the pulling guard or tackle is going to seal off the DE who's rushed in. You have to cut inside that DE or you're gonna be dropped, you can't bounce that to the outside.
A good play to run for a solid 3-4 yards is a traditional balanced two TE Ace Set. Run the Zone weak/HB Smash play, which runs behind the T. From there, if the play is designed to run behind the LT, you can flip it to run behind the RT, or if they're stacking the outside, audible to HB Dive, which is in the same formation, and will run behind the C/G Gap, which you can also flip if you choose. Thus, with one play called, you can audible to run to any of four holes based on what the defense is showing you without any of your players moving position. Just call the play, look at the defense, and audible to run at where they're weakest.