This is actually a problem with blizzard's UI and API as far as I know. Basically if you have 20g guild bank repair funds, yet your repair is 25g. It will not let you click the "Repair All from Guild Bank" button until your repair total is below the daily guild bank threshold.
Instead you must...
1: Turn off the auto repair feature in DurabilityFu
2: Repair manually piece by piece from your own gold until you are below the daily guild bank threshold
3: Finally repair all from gbank.