I seem to be unable to sync my game progress in Portal 2 to the Steam cloud. I have two openSUSE Linux machines with Steam, and Portal 2 installed on both; so I'd like to have a common state of savegames. After playing, cloud_log.txt says:

[2015-06-12 18:51:25] [AppID 620] AutoCloud done. Watching 9 files
[2015-06-12 18:57:32] [AppID 620] Running AutoCloud on exit. Looking for new and updated files
[2015-06-12 18:57:32] [AppID 620] Evaluating rule 1 with root="GameInstall" path="portal2/SAVE/76561198043128532" pattern=".sav" siblings="tga"
[2015-06-12 18:57:32] [AppID 620] Found 10 files that match /local/games/Steam/SteamApps/common/Portal 2/portal2/SAVE/76561198043128532/.sav
...
[2015-06-12 18:57:32] [AppID 620] Persisting file /local/games/Steam/SteamApps/common/Portal 2/portal2/SAVE/76561198043128532/autosave.sav to the cloud
[2015-06-12 18:57:32] [AppID 620] Persisting file /local/games/Steam/SteamApps/common/Portal 2/portal2/SAVE/76561198043128532/1434128240.sav to the cloud
[2015-06-12 18:57:32] [AppID 620] AutoCloud complete
[2015-06-12 18:57:32] Starting sync job
[2015-06-12 18:57:32] [AppID 620] Starting sync (upload)
[2015-06-12 18:57:32] [AppID 620] Upload failed due to conflicts in build list

I played Portal 2 as Windows version some time ago; could this cause the current issues when syncing?