A vendor record shows multiple lines of distribution with specific percentages. When creating a new invoice this distribution goes on to the invoice. When saving the invoice the distributed percentages change by small amounts.
This is due to the specific amount of the invoice, and how it splits with the percentages on the Vendor record. When the currency is set to round to 2 decimal places, the amounts round to make sure 100% of the total amount is distributed. The percentages on the invoice will then reflect the updated percents to 3 decimal places. The system is functioning properly to ensure the amounts are correct for the total amount of the invoice.