Suddenly Gift Certificate Purchases not Registering Properly

In our store, users may only buy gift certificates (GV) which are then depleted by actions in a sister site.

They can buy one or more GV and after a successful checkout, their increased GV balance should reflect the entire purchase amount. For the past 4 years all has worked well, now in the past 3 months suddenly only the first GV registers.

The code for updating the voucher appears normal but if a user purchases a $50 and a $100 only the $50 is added to their total or if they purchase a $100 and a $50 only the $100 registers. In other words, the purchase total needs to be saved (and once was) but is no longer. We have not modified any of the code in relation to this process.

Any ideas?

We have done a temporary work around of increasing the variety of denominations users may purchase and limiting them to single product purchases but we'd rather fix the issue as this is rather sloppy.