I had assumed the mod was displaying the correct amount.
Why doesn't it ?
Because Blizzard doesn't provide us with any way to get the correct amount except
1. Reading the NPC tooltip and figuring out the faction it is and then checking your standing with that faction.
2. Taking a diff of GetMoney() before and after repairing.
The only viable option is #2, but I haven't implemented it since I don't think it's necessary.
Two mods that perform #2 that will help you get an accurate assessment of the money actually spent, Rilynn. The Blizzard tooltip when you mouse over the anvil does not take into account any faction discounts you may qualify for, which results in the confusion:
& CashNotify (only this linked version from Incgamers I know works currently; you will also have to update the TOC to ## Interface: 20000 or later).
Both will show give you chat notifications of the exact amount of money you either spend or collect at any vendor or anywhere else. So you can confirm (after spending) exactly what the repair bill is without having to do math.
I've been using CashNotify forever; it works very well just for notification (but again, it will require you to do a TOC update before it can be used). AuditorFu is a somewhat bulkier mod (currently in development) that provides a lot of different money tracking features in addition to the chat notification.