Thanks for posting those photos !
This is a common problem related to the STOP bit logic and the asynchronous I/O scan of the ControlLogix / CompactLogix operating system. It's common enough that there might be comprehensive PLCTalk threads or Rockwell documents addressing it, but it's not my job to write those anymore, so I'll just wing it.
In A-B drives, a STOP command from any source prevents the drive from starting.
In A-B drives, START must transition from 0 to 1 while STOP is 0.
If the I/O connection RPI timeout occurs after the rung that sets .START = 1 but before the CompactLogix has gotten back around to the rung that sets .STOP = 0, then both .START and .STOP will go out in the Command word as = 1.
Even though on the next scan STOP has gone to 0, the transition of Start from 0 -> 1 was not done with STOP set to 0.
The easiest solution is to write your STOP logic so that it only asserts STOP if the .Running or .Active bit is true. That way STOP will stop the drive when you need it to, but it won't still be true when you send that 0 -> 1 transition of the START command.