Hi
Mine is working fine (GST rather than VAT - but setup probably the same).
This is my setup if that helps:

If using Items, you have the option on the item as to whether price includes GST:

Then invoice looks like this:

I then tried adding an extra line with a G/L Account style entry and it treated it the same way. I looked for specific settings against the GL Account and Sales & Receivables Setup, but couldn't see any setting that specifically drives that behaviour.
But then I looked specifically at the Customer - and that does have an option about inclusive / exclusive pricing:

Hope something in all this helps :-)
Cheers
Heather