I've tried using the built in kongregate plugin to submit my score but it doesn't show up on the website. I have it enable to display leaderboards.
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SOLVED.
Follow this guide: scirra.com/tutorials/9613/c3-submit-kongregate-statistic-eg-highscore-in-html/page-1
And when you edit the index.html file make sure you also replace the version in the .zip file before uploading to kongregate.