Just put two and two together about my comment here about an issue launching non-steam games actually being flatpak related as those were the items I checked. Didn't spend a lot of time investigating because the programs themselves ran fine launched from the desktop, just not from the steam shortcuts so I figured steam was the problem somehow and reverted to test. No issues at all after that.
Steam Hardware
A place to discuss and support all Steam Hardware, including Steam Deck, Steam Machine, Steam Frame, and SteamOS in general.
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Steam released another update that seems to have fixed it, so everything should be good now.
Great to hear that, thanks!