It appears you are right ! It must be a bug in Prestashop version 1.6.1.0
I didn't delete the tax rule, i just disabled it and made a new one, added all countries as you said
and selected the new tax rule in a product, voila ! prices on this product are back to normal (still missing the VAT included sign).
Since the taxes only apply for within EU and the products are too many.
Is there a way to make the original tax rules that stopped working, work again ?
If not, Is there a setting that would treat the "visitor" as someone coming from the origin country of the shop and display TAX at all times before someone decides to register ?