Color change on encoding

[Selur]

Since Hybrid guesses color matrix based on resolution, why did it changed colors since the video is 1920x1080 so BT.709 to BT.709 ?

Since you chose to ignore the sticky and provie details on how to reproduce the problem I can only guess.
If no RGB<>YUV conversion takes place color matrix does not matter.
If you do apply filtering, check the generated scripts to see whether something there seems wrong.
On playback RGB<>YUV conversion does take place so maybe the player of your choice it at fault.

Where is that option to save settings on close just to make sure it's disabled ?

"Config->Profiles->Auto save defaults"

Also, why does it say GBR while the source is BT.709 ?

<HybridData name="mkvColorMatrix" value="BT709"/>
and
<HybridData name="mkvColorMatrix" value="GBR"/>
differ.

Sounds like the value under "Config->MKV tagging->VUI->Matroska advanced video signaling" changed which do not matter if you haven't enabled the 'Matroska advanced video signaling'. No clue why the value before was GBR.

Going to bed soon, if you share proper details, I can try to find some time to look at it tomorrow after work.

Cu Selur