SteamDeck Kronos - polygons not displaying in Steam Retroarch, but works fine in Flatpak

Description

This is an unusual bug. Using the Steamdeck, Sonic Jam though Kronos works fine when using stand-alone Retroarch. But when I use Retroarch through Steam, Kronos displays no polygons at all in "Sonic World" mode. So even though both are running on Linux, there's a difference somewhere between the Steam and Flatpak versions.

Going through the logs, the only difference I can see is that the Steam version loads [INFO] [GLCore]: Version: 4.6 (Core Profile) Mesa 22.2.0 (git-17e5312102).(git-17e5312102), while the Flatpak version loads [INFO] [GLCore]: Version: 4.6 (Core Profile) Mesa 23.1.6 (git-0697ac0d75).

The issue exists even when forcing Steam to use the Windows .exe of Retroarch by forcing it to use Proton.

Expected behavior

Both the Steam and Flatpak versions to display the game correctly.

Actual behavior

Steam Retroarch doesn't work properly, Flatpak Retroarch does.

Steps to reproduce the bug

1. Load Sonic Jam (EU) on Kronos on Steam Retroarch.
2. Go into Sonic World
3. All you'll see is the world's floor - no characters, buildings etc
4. Repeat on Flatpak Retroarch, where it'll all work fine.

Version/Commit

You can find this information under Information/System Information

• RetroArch: 1.16.0

Environment information

• OS: SteamDeck Linux

Start by reproducing Sonic Jam (EU) in Sonic World on Steam RetroArch and Flatpak RetroArch on SteamDeck Linux. Compare the GLCore logs, especially the Mesa versions, and investigate the Steam and Proton configurations mentioned in the report. Done means characters and buildings render in Steam RetroArch as they do in Flatpak.