The VAT rounding/Invoice line setting in Invoice settings (at System > General > Settings) is now applicable to multiple tax amounts. Previously, this setting was applicable only to a single tax amount.
When you enable the setting, the VAT amounts in the invoice lines are rounded up. The total VAT amount then reflects the sum of rounded VAT amounts in the invoice lines.
For more information, see Product Update 419: VAT rounding/Invoice line check box added to Invoice settings (Italian legislation).