I've had a similar issue with stable (non-beta) steam client and Factorio. I had cloud saves enabled globally, but I disabled them for Factorio specifically and I still get this issue sometimes. Restarting steam usually helps with this. I think I had this issue with other games too in the past.
Just insert a skip button, when this happens.
I missed many Rocket League Tournament because of this...
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Your system information
Please describe your issue in as much detail as possible:
While Steam Cloud is syncing a game with large save files (in my case Factorio) through a slow connection, i can't run another game (that also makes use of the Steam Cloud) as Steam just opens a dialog box "Preparing to launch..." and stops the game from running until the sync is finished.
To be sure, I have turned on the setting "Allow downloads during gameplay" globally, but it doesn't seem to affect the Steam Cloud sync.
I know i can just disable Steam Cloud manually for any game, or wait for the synchronization to finish, but it just shouldn't work like that.
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