I also use the same power supply, and have faced similar problems mainly when using the Flying Bus.
I switched to the Noise Filtering Power Distro board and miraculously this corrected the problem. This is powering 2 rows of 104HP using 2 distro boards daisy chained via the molex cable. Has worked like a charm. Also, if you plug your ribbons in backwards you will also get the flashing lights thing. This is a protection mode that it goes into to prevent you from frying your modules, so I would examine that as well..

Hope this helps, good luck!