Hello and sorry about the trouble! I would be happy to help you out with some troubleshooting steps.
For Steam:
1. -Try verifying Clone Drone's file integrity through the Steam client.
And if that comes up fine:
2. -Try holding "S" during Clone Drone's startup and pick the reset save option.
This will allow Clone Drone to regenerate any possibly corrupt save files, and if that still doesn't solve the issue:
3. -Try disabling the Steam overlay for Clone Drone through the Steam client.
Sometimes the overlay causes some delays in the menu loading. And the last thing I can think to try in case none of the above works:
4 .-Try disabling Steam Cloud Sync for the save files through the Steam client.
That one is a long-shot but synced saves may be interfering with your settings.
For itch:
There might be something else going on but holding "S" might help. Let me know if you are using this version exclusively and I can brainstorm some things to try.
Sorry once again for the issue, but hopefully we are able to get you up and running quickly!
-Cheers