Assuming your mapping for Outputs is V2030-V2061, then B2056.2 would certainly be the Suspend Output bit. If this bit is SET (ON), then the CTRIO immediately stops output. It could be if the operator is using an HMI device for the "pause button" which then in the ladders gets translated to a SET B2056.2, that there is some delay in communicating to the PLC this button press from the HMI. You might want to test the machine using DirectSOFT's Data View and verify when the operator presses the "pause button" that this bit gets set. Or you might want to set the bit manually to see if the CTRIO stops. Or is the CTRIO stopping, but the momentum of the machine carries it forward further?
Does this help?