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I'm having the same problem as the two above. I can't tell you how many different things I've tried, how many videos I've watched, and how many times I've tried a fresh install. No matter what I do, I cannot get the Pixelmon to spawn. While I can see the sidebar and the items - if I'm in creative mode - I do not get the starting blue screen where I can select my first Pokemon, and cannot actually craft any of the Pixelmon items or blocks.
To those above, a lot of people are suggesting that you should not only put the Pixelmon .zip in your server's mod folder, but also unzip the assets and pixelmon folders into your main server folder before deleting your world folder and restarting the server.
I guess for a lot of people that fixed the issue, but it didn't for me. If anyone has more light to shed on this situation, it would be much appreciated.