Hi DavidD
You can email the screenshot to support@method.me and we can have a look at it. I've had a bit of a play with customizing the Invoice screen and think I might know the cause.
In the Invoice Line Item grid do you still have the % column? If this column isn't present it doesn't treat the value as a percentage regardless of how the item is set up.
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If this is missing and you want to re-add it you can follow these steps:
Step 1 - Edit your custom invoice screen then edit the InvoiceLineItem grid
Step 2 - Add a new column as below and move it to just under the Rate column
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Step 3 - Scroll up to the Item column and click Actions
Step 4 - Change the Event to Text Change, scroll to the bottom of that list of actions and Edit the 'Retrieve Value From Table - Get IsRatePercent' action
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Step 5 - Set the action as below
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Step 6 - 'Save & Close', 'Save & Close', 'Finish' and 'Publish'.
With a little bit of luck that should get your discounts to now act as a percentage. If anything above isn't clear or you have further questions just let me know.
Jeff