1.1.0 RC8 Steppers Twitching Every Second

I'm having an odd issue after updating my firmware from 1.0.2 to 1.1.0-RC8 compiled under Arduino 1.8.1. Upon updating the firmware the first communication attempt is interrupted:

READ: echo: Last Updated: 2016-12-06 12:00 | Author: (none, default config)
READ: Compiled: Jan 13 2017
READ: echo: Free Memory: 3740  PlannerBufferBytes: 1200
READ: echo:Hardcoded Default Settings Loaded
READ: echoteps per unit:
READ: echo:  M92 X80.00 Y80.00 Z4000.00 E902.29
READ: echo:Maximum feedrates (mm/s):
READ: echo:  M203 X300.00 Y300.00 Z5.00 E25.00
READ: echo:Maximum Acceleration (mm/s2):
READ: echo:  M201 X1000 Y1000 Z5 E10000
READ: echo:Accelerations: P=printing, R=retract and T=travel
READ: echo:  M204 P500.00 R500.00 T500.00
READ: echo: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)
READ: echo:  M205 S0.00 T0.00 B20000 X20.00 Y20.00 Z0.40 E5.00
READ: echo:Home offset (mm)
READ: echo:  M206 X0.00 Y0.00 Z0.00
READ: echoID settings:
READ: echo:  M301 P22.20 I1.08 D114.00
READ: echo:Filament settings: Disabled
READ: echo:  M200 D3.00
READ: echo:  M200 D0
READ: echo:Z-Probe Offset (mm):
READ: echo:  M851 Z-2.50
  Testing plaintext communication protocol...
  Testing binary communication protocol...
  Testing alternate communication protocols...
READ: echoD init fail
READ: ok
WARNING: CRC mismatch detected
READ: 
  Attempting RTS reset and trying again...
  Connection failed.

The next attempt at connecting is always successful.

Even before connecting, both Z steppers and the X stepper make periodic clicking sounds every 1 second. The affected steppers make a clicking sound but don't appear to be moving. The extruder stepper and the X stepper are unaffected. When I try homing any axis, the stepper motor being commanded will start to home but will be interrupted by the periodic 1 second issue which interrupts the homing and causes the motor to stop and then start moving a tiny bit every second toward home.

I had no issues with my hardware and Marlin 1.0.2 so I'm curious if anyone else has run into this issue. I'm certain it's a firmware bug or configuration error because it was present on my previous RAMPS 1.4 setup which has been replaced with a RAMBo 1.3 board. I'm stumped

For what it's worth I think I found the problem. In my configuration.h file I had the following three lines uncommented. I don't recall why but after commenting and disabling their function the twitching issue is gone and the motors move normally again.

#define ULTRA_LCD
#define SDSUPPORT
#define SD_CHECK_AND_RETRY

I'm not sure what the third option does, but that could explain the periodic nature of the issue/interrupt I was seeing.