Hi,
I've noticed that the problem is the way the cloud sync is namig the savegame directory.
When I start PoE on a new machine, it creates the savegame files in
~/.local/share/PillarsOfEternity/SaveGames
Steam cloud sync installs the synced savegames in
~/.local/share/PillarsofEternity/SaveGames <-- note the little 'o'
I worked around this by replacing
~/.local/share/PillarsOfEternity/SaveGames
with a symlink to
~/.local/share/PillarsofEternity/SaveGames
This solution wil most likely break when the issue is fixed though. HTH!