The GCLK0 pin glitch occurs when the configuration controller passes control of this pin back to the fabric. This is the only global clock pin affected because the GCLK0 pin can be used by the configuration controller as the external configuration clock for master modes (USERCCLK).
During the passing of control from the configuration controller back to the fabric, the voltage rail driver in the I/O has to be changed if one of the above mentioned I/O Standards is not used.During the transition of the voltage rail driver, if the pin receives a logic high and the fabric signal dips to Vil, max., the fabric will see a glitch low until the voltage rail driver switch occurs and the logic high is restored.
To work around this issue, critical logic can be delayed or reset after configuration, or moved to another clock input.The I/O Standard can also be set to one of the above mentioned I/O Standards which does not cause the voltage rail driver to switch and eliminates the glitch.