The "Continuous" mark is always checked after loading the game, no matter how it was before.
The game is probably resetting the flag on incubator object to TRUE at game loading, overwriting the previous value.
Steps to Reproduce
Construct an Incubator -> set the incubator to any egg type -> unmark the "Continuous" check -> Save game -> Reload
This issue has been fixed in either a future version or updated in a previous version.