Possibly related to ticket #17255, as they are dealing with one of the same Pixelmon config options. The in-game Pixelmon Config menu considers 1024.0 to be the default Raid Shiny rate for 5 star raids even though the actual default Shiny rate for 5 star raids is 512.0.
Whenever you start a world, the Shiny rate for 5 star raids is 512.0. However, whenever you Reset to Default the Raid Shiny rates in the Pixelmon Config, the Shiny rate for 5 star raids becomes 1024.0. This doesn't stick due to the bug in ticket #17255, but it still stands that the game erroneously claims that 1024.0 is the default Shiny rate for 5 star dens even though a new world will have 512.0 as the 5 star den Shiny rate.
How to reproduce:
1) Create a new world
2) Open the Pixelmon Config
3) Click "Raids".
4) Look at the Raid Shiny rate. The Shiny rate for 5 star raids should be 512.0 in the config settings.
5) Click the button to "Reset to Default" next to this config option. The Shiny Rate for 5 star dens should have become 1024.0.
Tested using The Pixelmon Modpack in CurseForge