Box 3 will be highlighted in red when it is not equal to the sum of boxes 1 and 2. This is most commonly caused by a formatting or rounding issue or not linking all the boxes. VAT Filer will not calculate the boxes, it will only use the figures you enter on your source spreadsheet.
Please check the formatting of the cells for boxes 1 through 9 on your source spreadsheet to ensure they are set to number with 2 decimal places.
After any changes, please relink to the VAT Filer so the values then update and try your submission again