This is a known issue in 13.3 which could result in seeing behavior where the IBERT GUI shows the GTX as LINKED, but the QPLL shows as NOT LOCKED. The QPLL could actually be locked, but the tool does not know this since the QPLL Locked status is not being read periodically.
To work around this issue:
This triggers a read from the COMMON block inside the IBERT core which reads the correct QPLL LOCKED value.
This is a known issue in 13.3 and is scheduled to be fixed in 13.4.