If the bowls are over-flooding still, the little valves that the floats operate are not closing properly while the engine is vibrating.
If that is happening, the level inside the bowls is correct at start ups but increases until making the mix too rich and over-flooding.
http://faq.ninja250.org/wiki/How_do_..._the_floats%3F
http://faq.ninja250.org/wiki/How_a_c...Floating_In_It
Sometimes the little neoprene pointy thing gets too hard, sometimes it is just deposits on the seat of the valves.
Close the petcock after the engine starts and check if the same thing happens during a long idle.
If not, it is the float-valve(s).