I'm not sure what state(s) you are looking at, but I am in the midwest, and most of the programs I am finding are two years for MOT. I know that some programs that are three years are because that school also has a bachelor's in OT and the first year of the MOT is getting caught up with the classes that those with a bachelor's in OT have. There aren't many of these programs anymore... hope that helps!
After a little searching it seems that most programs are two years (or just over 2 years). I'd say keep looking, and you should be able to find a similar program in your area.