It is definitely caused by this subroutine at $582E.
Some more information:
It's used whenever entering a new screen and seems to do something with palettes(?). Any advice or interpretation is most welcome.
Reducing D3 from 10 down to 02 yields this:
10 down to 0B: normal
0A: green AICOM logo disappears
09: yellow logo disappears
08: blue line disappears
07: orange PULSTAR title disappears
06: lighter orange copyright text disappears
05: unknown
04: unknown
03: light blue text
02: grey text
Lowering D3 also naturally reduces the loop count and directly affects how long it takes the OSSC to find a stable signal, making the image re-appear faster when entering a new stage.
Any clue as to why this is occurring?