When I monitor the intervals between two adjacent rising edge of Active Video the intervals can vary by 2 clocks.
For example, with 720p60 Active Video, the interval is 824,826,824,826....
How can I resolve this issue?
This is a known issue in HDMI RX Subsystem IP which has been fixed in Vivado 2018.1 and later versions.
All users should upgrade to the latest Vivado version if possible.
Vivado 2017.3 and 2017.4:
You can work around the problem by adding the attached custom IP (2018-05-10_-_AR69184_-_v_hdim_rx_tr_v1_4.zip) to the native interface of the HDMI RX Subsystem.
It can be used to correct the video timing, so that the distance from the active video to the HSYNC is always constant.
Vivado 2018.1 and later versions:
The issue has been fixed in Vivado 2018.1 and later versions.