Upgrading from Marlin 1.0.0 to 1.1.0 RC3 causes X/Y skipped steps (3 replies)

I have a modified leapfrog, ramps 1.4, CW230 stepper drivers. Its always ran Marlin 1.0.0 great. I added a full graphic smart controller so I dont have to tether my laptop anymore. To get that working, I upgraded to Marlin 1.1.0 RC3.
I went through carefully moving all the correct settings from configuration.h to the new one. Everything so far is working great, except my X and Y axis skips steps and causing heavily skewed prints.

Here is what I'm seeing with only 2 layers.

Acceleration and jerk values were double checked the same as the old firmware. I also tried reducing speed, accel, and jerk down as much as 25% normal, but the issue persists in a lesser amount.
For now I'm back to 1.0.0, and its working fine.

Here is M503 from the old firmware:

Steps per unit:
M92 X33.33 Y33.33 Z200.00 E52.20
Maximum feedrates (mm/s):
M203 X200.00 Y200.00 Z160.00 E45.00
Maximum Acceleration (mm/s2):
M201 X1000 Y1000 Z50 E10000
Acceleration: S=acceleration, T=retract acceleration
M204 S1000.00 T1000.00
Advanced variables: S=Min feedrate (mm/s), T=Min travel feedrate (mm/s), B=minimum segment time (ms), X=maximum xY jerk (mm/s),  Z=maximum Z jerk (mm/s)
M205 S0.00 T0.00 B20000 X15.00 Z0.40 E5.00
Home offset (mm):
M206 X0.00 Y0.00 Z0.00
PID settings:
M301 P36.49 I2.95 D112.99

Here is the new:

Steps per unit:
M92 X33.33 Y33.33 Z200.00 E52.20
Maximum feedrates (mm/s):
M203 X200.00 Y200.00 Z160.00 E45.00
Maximum Acceleration (mm/s2):
M201 X1000 Y1000 Z50 E10000
Accelerations: P=printing, R=retract and T=travel
M204 P1000.00 R1000.00 T1000.00
Advanced variables: S=Min feedrate (mm/s), T=Min travel feedrate (mm/s), B=minimum segment time (ms), X=maximum XY jerk (mm/s),  Z=maximum Z jerk (mm/s),  E=maximum E jerk (mm/s)
M205 S0.00 T0.00 B20000 X15.00 Z0.00 E5.00
Home offset (mm):
M206 X0.00 Y0.00 Z0.00
Material heatup parameters:
M145 M0 H185 B60 F255
M145 M1 H230 B100 F255
PID settings:
M301 P36.49 I2.95 D112.99 C100.00 L20
Filament settings: Disabled
M200 D3.00
M200 D0

Any idea whats going on here? I'm thinking a driver pulse width issue, but I'm not sure where to start.