I/O glitch was observed on bank 2 of a blank device before programming. On a blank device, the I/Os are placed in the Flash*Freeze state (tristate with weak pull-ups). When the programming starts, the I/Os transition to the boundary scan mode. On I/O bank 2, there is a race condition between exiting the Flash*Freeze mode and the entering boundary scan mode. During this transition, the outputs on bank 2 briefly drive high until the boundary scan mode is enabled. This transition results in an I/O glitch.
To prevent this glitch, use the JTAG command to adjust the I/O drive strength to zero before programming starts.