Sounds like miscommunication to me, as opposed to her trying to use those days however she sees fit.
I am wondering; if she did not give you a new cheque in May, to account for those missing days, why this issue did not come up then. I know hindsight is always better, but I would likely have dealt with it right then.
Was there confusion in that, when you did not get a new cheque, perhaps you thought that meant that she was fine with just forgetting about those days. (I am sorry, my question mark does not seem to be working, LoL)
Honestly, I would let this slide. I know that you do not like that it seems as though SHE is dictating things, but this is money owed to her, and a month overdue. Perhaps just a gentle reminder that in the future, the adjustment will made to the NEXT months fees, not carried over. Play it to her advantage, in that you would hate for them to miss out on these banked days if they waited too long to use them.
Hope that your hubby is better now.