Hello @drewboardman, the selection and management of compatibility tools is handled by the Steam client, not Proton itself, so I've transferred this issue report to the steam-for-linux issue tracker.
Can you list some specific examples?
Also, with the per-game compatibility tool override removed, can navigate to a couple affected games, then select Game Info and under the Steam Deck Compatibility line, there should be a line that reads something like Runs on this computer via Steam Play. Proton # selected by Valve testing. Please check that line and note what that reads as.
I actually just uninstalled GE-Proton, because the issue was so persistent. One example game is "Tiny Rogues". Right now, after removing the compatibility override - it reads 8.0 -2.
Nothing extracted yet.
Compatibility Report
multiple games
System Information
Steam Deck
Symptoms
This seems to indicate that proton version, listed alphabetically, are defaulting to the first in the list (even with compatibility not set manually). Is there a way for me to confirm this suspicion?
Reproduction