Ok i figured out the problem.  Cash control should be clearer.

Taking Money Out or Putting Money In, doesn't really refer to the Cash register, even though it reads as if you are putting into or taking from the register as the dialog box shows.  So here is what happens.  

You end your sales session like this:

Theoretical is 97.18

Real Balance is 0.00

Difference is -97.18

So you count the money in the drawer and find only 97.00.  You now have a difference of 18 missing cents in the cash drawer.  So you decide to:

PUT MONEY INTO THE CASH REGISTER as the dialog says.  So you put in the missing 18 cents and you get this:

AHA!  If you notice, you actually added the extra 18 cents to the Theoretical Closing Balance, not to the Real Closing Balance.  The Real Closing Balance would be the cash drawer, not the theoretical one.  You can prove this by doing the opposite.  You now have 36 missing from your REAL cash drawer as can be seen, so you need to TAKE MONEY OUT.  It doesnt make sense at first because the dialog says you are taking money OUT OF THE CASH REGISTER but you are NOT!  This actually means you are taking money OUT OF THE THEORETICAL.  So you take out the MISSING 36 cents:

So I can totally see how I have to think about this and re-train my employees.  But Im worried about the effects in accounting, if Cash Control is somehow accounted for in the system (which would be nice btw, but I haven't gotten into that yet).  Because what we are saying is that there are 36 missing cents from the cash drawer, which might mean someone stole them, but we are messing with the actual transactions total!  We ended up saying that we only made transactions for 20.00 when in reality we made transactions for 20.18! 

This is terrible!