I have been having an issue with prices rounding up but only when the price is £39.99.
I am using version 188.8.131.52 with Unicenta and the plug-ins to get the databases to sync.
In Unicenta if I change the price to £29.99, it will show up on magento correctly.
When I put in £49.99 it shows it correctly to.
But when I change it to £39.99, it will show up as £40.
When I originally set the server up everything was working (tax wise) I reloaded the server (VPS from OVH) as I realised the pictures I was using for products in Unicenta was to big and causing database issues and failure to open up the products menu in unicenta. But the fault is still showing.
I am fairly sure that the tax is all set up correctly in Magento and Unicenta.