The direct input GT reference clock coming from the IBUFDS might not be stable even after GTPOWERGOOD is asserted.
This condition causes two possible issues for IBERT:
When generating IBERT designs that use the CPLL_CAL block (used with CPLL and internal system clocks), there could be an IBERT detection issue after the bitstream is downloaded into the device using Vivado hardware manager.
The PLL might not lock for UltraScale GTY designs with a CPLL configuration when the quads used are not consecutive (for example, quads 225 and 227 are used, but not quad 226)
Issue 1 resolution:
Use a JTAG TCK frequency less than or equal to 6 MHz for IBERT designs that use both an internal system clock and CPLL.
Issue 2 resolution:
This applies to IBERT designs that use both an internal system clock, a CPLL, and non-consecutive quads.
Use a JTAG TCK frequency less than or equal to 6 MHz AND use a configuration with consecutive quads (for example, quads 225, 226, and 227) rather than non-consecutive.