For some reason Samui immigration don't like giving out Non-O's...my friend had exactly the same problem there a few months ago, he did end up with his Non-O, but it took quite a bit of persistence. It was eventually resolved when he got to speak to the boss lady in the left hand side office. The counter staff flat out refused and told him the same as you.
He had letters from Bangkok immigration, and Surat Thani immigration telling Samui to issue the visa, but they still resisted, it wasn't until he got to speak to the boss that it was resolved and he got his Non-O