Hi I am a UK national on a 2 year J-1 visa as a post-doc. I believed that under article 20A (I am conducting research) of the UK-US tax treaty that I would not have to pay tax while I am here. But the institution who is administrating the post-doc are withholding 14% tax on my stipend payment saying that under article 20 because the non-qualified scholarship comes from within the US.

When I told them about article 20A and that I am conducting research and not in a education program they then stated that article 20A still does not apply as they are not an accredited educational institution.

Should I then be paying tax or not?

If the company for whom you work as a researcher says they are NOT an accredited educational institution, then it is likely they are right and you need to be paying the tax.