Tony,
Good flats can be difficult. Typically you want to try to bring the average ADU count of your histogram up to 50-75%. Although you want to have the flats taken in the same orientation, they don't need to be the same exposure length or exposure on the histogram.
When taking flats on my refractor I take 25x5s through each filter. Takes about 45-60s with narrowband though. With my DSLR I can do them at 1/100th second.
I have a feeling that it may be you not exposing the flats enough, 50-75% of saturation