I've just been to Phnom Penh to get my non B visa, successfully, but thought I should post this.
When I was at the Thai Embassy in Phnom Penh I was told they couldn't give me the non B because I hadn't applied for my work permit in Thailand. This was contrary to all other info I'd been given, and I'd have had to go back to Thailand again on a tourist visa before returning to Phnom Penh, but I was very lucky because my Thai friend who accompanied me knew people in the Embassy there, hence I was eventually ok.