My Wife is a Filipina too and I am British, the way we did it was for me to get my retirement visa and my wife had a student visa to learn Thai, once she finished her visa which was 6 months she was allowed to 'follow' me on my retirement visa, best thing to do is speak to these people here, they was very helpful.
I had the same in Hua hin, after nearly 3 weeks of waiting I went back in and was asked to go to the managers office and there was a clerk there sifting through a huge pile of papers to find mine, got it sorted within 20 minutes after that.