When you are checking values in a checkbox set the values only get committed (or saved) when you exit that field, or commit it manually.
What I would do is attach a script trigger to that field on the "OnObjectModify" event.
The script trigger should be a simple "commit record" script step.
That way, the moment you modify the value of that field (check a box) it get's committed (saved)
In layout mode just right click the checkbox set and go to script triggers.
If you have any more questions make sure to let us know.