Magento 1.9.2.x issue with double taxation - IMH Hosted

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I have a magento installation, and a customer pointed out that our site was incorrectly calculating taxes.

If you go to substance - europe .com and add an item or more (that's not a sample, eg Free) to the cart, and then view the cart or continue through to checkout, you'll notice a very weird issue.

Let's say the product is 259.95
Tax is 20% (VAT, UK)

Subtotal: 259.95
Grand Total Excl Tax : 311.94
Tax: 51.99
Grand Total Inc. Tax: 363.93

It should however, read:
Subtotal: 259.95
Grand Total Excl Tax : 259.95
Tax: 51.99
Grand Total Inc. Tax: 311.94

It adds the amount taxable to the 259.95 and includes that value in the excl tax price. Then it adds the tax again and adds it to the grand total inc. tax line.

I have been through multiple sites checking setup.
The setup i have is:
** All settings are noted to be excluding tax
** Tax calculation method based upon total
** Tax calculation based upon Shipping Origin
** Apply Customer Tax before discount
** Default Tax destinations are set to UK (it's a UK site, this is correct for this install)

I've also reinstalled all the core files
I've also disabled all extensions.
I've also reverted back to the default theme.

- None of the above has fixed the issue. Followed all the UK setup tutorials and it just doesn't work correctly. The weird thing is, it used too. I don't know when it stopped working, it was only today that a customer pointed this out to us.

- One anomaly, if I do paypal checkout it passes through all the correct information.
Hello Mdowner217, This may be a long shot but try what is described in this StackOverflow Thread as they are having a slightly similar issue. Please let us know if this solves the issue at hand. Best Regards, TJ Edens