The Concurrent mode option in the software allows for multiple devices to be programmed at the same time as the algorithms can take advantage of the wait times required for 1 flash and operate on another flash device.
This option is turned ON by default in the GUI and changing the preference will not disable this feature.
This issue has been resolved in 10.1 SP3.
To work around this issue, select only 1 device at a time to program. If multiple devices in a chain must be programmed, their operations should be completed sequentially.