What addons have you installed?
Is this an upgrade from a prior version? which version(s)? Or is it a fresh new install?
What payment modules are enabled? What order-total modules are enabled?
What are all the settings in your ot_gv order-total module?
Was this transaction paid-for in-full by the gift certificate? or was there a balance that was paid via some other module? which one?
If I am to attempt to recreate your environment and recreate the exact same conditions as yours, what do I need to do to my fresh clean install to make it function just like what you've described?