Server is running Pixelmon 5.0.0 and Sponge for Minecraft 1.10.2.
Rayquaza seems to be only spawning in Ocean Biomes during Dawn/Dusk. The chat announcement says Ocean and it spawns in it aswell.

NOTE: Server was transfered from 4.2.7 and then into Beta 12. Worked fine in both versions.

are you using Spawn of Psyduck? if so then update it

Thanks, Ill let the server owner know and we'll give that a shot.

I deleted all the config files, did /psyduck reload in-game to regenerate a new config.

It now shows 6 Ocean Biomes for Rayquaza, so it's definitely a bug.

Using the Dec.24 Version

I have tested this and it is a bug with spawn of psyduck that is not only limited to Rayquaza. Even in the most recent release of SOP, if you check the biome of any pokemon they all have Ocean as one of their biomes. I also created a superflat ocean world with a large platform for pokemon to spawn on. When I had SOP installed every type of pokemon was spawning on it. However, when I removed SOP only the regular water-type pokemon spawned on it. I would recommend removing SOP until it is fixed and just using the wiki to look up where the pokemon spawn.

i specifically fixed a bug with Ocean biome being used in the latest version, you must have an invalid biome name listed (eg i had written Prarie instead of Prairie) as it Minecraft defaults to providing biome 0 when the specified biome name cannot be found

I'm the owner of the server that this ticket came from and I have the latest version installed with a fresh new config because I never used this plugin before.

okay, i'm looking into it now

Okay, i immediately found the issue, it's broken in non-Biomes o Plenty setups, fixing it now

For posterity:
To resolve this sinply delete all the biome names in the non-Vanilla list for each entry (deleting the list itself will just mean it gets reloaded next config reload)