Sometimes when designing the board, it is possible that the board designer has swapped the TMDS polarity to make the routing easier. In this case, the Video PHY Controller /HDMI GT Subsystem must be configured accordingly. When the polarity is wrong, the system will have difficulty detecting an incoming video stream, even on those common resolutions (for example, 1080p60) and the detected timing can be far from the expected value. You should start looking at the data pins for the GT being routed to the FPGA to check whether they have been swapped.
An API is available in the Video PHY Controller /HDMI GT Subsystem driver to allow you to set the polarity. If you experience system behavior as described above, you can use this API to change the polarity to confirm whether it is polarity swapping that is causing the system issue.
u32 XVphy_SetPolarity(XVphy *InstancePtr, u8 QuadId, XVphy_ChannelId ChId, XVphy_DirectionType Dir, u8 Polarity);