Hey there,
I tested in Singleplayer if Pokémon can be catched (it worked), after that I gave that to a Server Admin who updated the pixelmon version from the Server. Now I had time and tested it on the server.... but this time it won't worked.
I spawned in a extra Minecraft Overworld, added by the Plugin from the Server, a rattata with /pokespawn rattata and fighted it with a Lugia of my team, without damage it, I tried to catch it with a Pokéball.
Like in the previos version the ball disappeared into nothing.
After that I tried in the same dimension it again with all same steps as before, just threw a other ball. (a Master Ball this time.)
Same thing happened.
Now, I nearly just thought it was the dimension who was bugy, so I ported to the main world created by minecraft it self.
After following all steps allong like before... same thing happend. The ball disappeared into nothing after the 4. "tick".
The Server Config is the same on the client, cause the Launcher is linked up with the server. With that knowledge I go to the Singleplayer to test it there, if there is anything wrong in the config.
This time it works.
So it maybe gives still a problem with catching Pokémon when there are mutliple dimensions.
Here the Log from my server try:
https://pastebin.com/LTdZjg12Hope that bug (if it really is one) can be fixed.
~Soldier4ever