Why would cloning a site that works great to make a new one cause issues? To me that is the safest way to make sure it is all working and havent had any issues doing this before. I appreciate your suggestion though, not sure my phpadmin skills are up to it to be honest, massive nightmare.....
I do not know why or what. It may not have anything to do with cloning. However I know that my method will help identify and possibly resolve issues.
By making a completely new test installation - you take settings back under your control and go back to a "clean" install.
Porting over a few VM product category manufacturer tables is easily achieved - simple export - import using Heidisql
I am NOT suggesting doing this test on a live site!
Maybe someone here knows of a better way to identify or resolve this particular issue. In the time it takes to wait for a better suggestion - you could get a new test site created and tested.
I am sorry this may not meet a "quick fix" just hit this button solution - but clearly all other suggestions below have failed and you started this thread on June 20th
By now you may have had it all working perfectly - language/payment etc.