Just a quick thing to check:
Most probably you are already doing it, but a lot of developers that have problems with saving and loading (System Save or Local Storage) are because they dont wait until the save is complete as it takes more than a tick to do the job. Have a look and make sure you wait until the save is complete. You can use the "Wait for the previous Actions" or the triggers that C3 offers.
If you dont wait properly, that could explain why sometimes it saves properly and some not.
-As when it saves correctly maybe it is because the save happens quickly
-But when it doesn't save correctly it is because needs more time to save and if you dont wait it will mess up the save.
Example:
-You use the Actions SystemSave
-The next action is to move to a different layout
Note:
The same thing is true for loading saves, you need to make sure it waits until the save is loaded