I had this problem before. I think it had to do with the size of the flat being incorrect. I believe it has to be 32 x 32, 64 x 64 or 128 x 128 and so on. Apparently you can have flats as big as 2048x2048, I don't know what you use to get those big of flats to work, but you probably wont need anything that big.
Make sure you saved it as a doom flat and have the F_START and F_END markers in the right place.