Hi guys,

I'm currently playing as Sophon and every once in a while the game will prompt me and say I have access to a new resource, like Jadonix, even though I cannot see it anywhere. Am I missing anything?

These messages are basically telling you that your empire has discovered a new resource. It's likely that you received some of the resources as a reward from searching a curiosity, or gained a new minor-faction population in one of your systems. Every faction has its own preferred luxury resource that can be used to double the effectiveness of their traits and increase their reproduction rate. When you obtain a population from a faction for the first time, your empire will discover their preferred luxury if it hasn't already.

The message really needs updating. Previously, you didn't 'discover' resources like this (from minor race preferences). I'd suggest amending the message or reserving the message for discovering resource deposits (or stumbling across a cache of them, or whatever).