I don't know if this is a buggy thing that needs to be reported or if there is a coding solution or not.
As I have been playing around with this it looks like what is happening is when a new instance of the subForm in added and put in the right place it assumes values of the check boxes from the subForm that was in that position previously. They can't be unchecked. At least that is what is happening in Preview mode.
It looks like they just have the appearance of being checked but really aren't. I'm just guessing at this point but it seems like that is what is happening. I have noticed that when it gets to the point where a so many new instances are added that a new page is added then the check boxes that have the appearance of being checked are no longer checked. Strange.
I suppose I could post the form if anyone is interested in seeing how it is working.