Solved Jerk Settings - Marlin Firmware Upgrade

I started having the exact same issue immediately after upgrading to 1.1.7 from 1.1.1. My prints were printing perfectly on 1.1.1 and I was able to control acceleration and jerk without problem. I'm using S3D. As soon as I upgraded to 1.1.7, the jerk and acceleration seemed to have gotten so much worse, despite the fact that I have both configured in S3D and starting script. I was printing at 90mm/s before and getting great results. Now I can't get anywhere near that speed without running for cover. I haven't tried tried any other slicer besides S3D since the firmware upgrade. The thing is, I always override jerk in my startup gcode. I have it set to 17 and always have, and as for acceleration, I set the outer perimeter to 500, and everything else ranging from 1500 - 2500 with great results. The new firmware seems to interpret these numbers differently than the old one. I can see in the terminal that the acceleration is being changed where it's supposed to.