Erratic Rotary Encoders Since 6.4.13 Update

Since the most recent update has been pushed out, the rotary encoders on FarmBot have stopped working reliably. It started when the steppers kept trying to move even after hitting the belt clips on the x axis. I was able to navigate around the issue at first by toggling from 1.3 to 1.4 firmware for the Arduino and then I had to disconnect from power and run a new calibration sequence.

Things had been working fine, but it suddenly stopped in the middle of testing a watering sequence. The FarmBot was then showing that it was in the home position even though it was stuck in the middle of the x axis. I have found the the rotary encoders for the x-axis are the most unreliable for some reason. Is there a bug in the firmware? Do I need to recalibrate after powering down and on again? Please advise.

FarmBot axis length, determined during calibration, is saved across power cycles. However, when FarmBot regains power its position will be zero. This means calibration only needs to be done once, while “find home” should be run before performing actions after startup. “Find home” will move toward the home position until the motors stall and set that position as the new home (zero).
If FarmBot’s position resets to zero in the middle of a sequence, either power was lost or a “find home” command was run and the motors stalled. Some potential solutions include replacing “find home” commands with absolute movements to zero, fine-tuning motor settings to reduce stalls (such as reducing motor speed or adjusting acceleration), or modifying the encoder settings to reduce sensitivity. See the encoder troubleshooting FAQ for additional troubleshooting information.
If you are using v1.4 hardware, v1.4 should be selected as the firmware. Other selections are incompatible, so
they will cause the encoders to stop working