another reason was that their system identified some mail account as fake and despite confirmed booked they were refused. I had one customer. That should be a thing of the past.
There was, last week, a scam exposed on various Filipino Facebook sides involving a Company in Bangkok that cooperated with a company in Phuket to obtain fraudulent Non B, so they check documents and they also check with airline about the booking of flight. If you plan to use our service, please make sure that all in order. Savannakhet is aware of these things.
The staff advised various customer from Phuket and Pattaya that they can not get Tourist visa here if warning stamp in passport, obviously your case is different, but I can not ask now. He mentioned as long as paperwork is OK people can apply Non Immigrant there.