I think I figured it out. I applied funds A and B to reservation X, and that worked fine. Then I applied B and C to reservation Y. B was initially short by the amount of A.
The case where two changes occurred was an extension of this, with the missing funds being equal to the values of two small PNRs I had applied on reservations I made within the few preceding minutes.
Its important to note that your outbound and return flights each have a dollar amount attached to them, and while you are processing an exchange to a new reservation the entire amount of each coupon can be tied up until processing is finished.
for examply if you had an outbound and return each worth $100 ($200 total) and you were booking a new reservation for just $50 - you would expect to have $150 more to add to another reservation. and you will, once your $50 reservation is completed. But, until its complete you would have $100 because your outbound funds would be tied up, but your return funds would not. Essentially, your outbound flight just became a $100 bill, and you have to wait for the cashier to give you $50 in change before you can go next door and make another purchase.