You may have just hit the nail on the head there!
I leave my refractors dew shield fully extended when taking flats, this may be the issue as it leaves about 15cm between the lens and the light source. I will have to wait for a break in the weather to go out any try some with it retracted.
Its funny, if this is the cause, i actually learned this lesson a couple years back with my EF200L lens, that flats without the lens hood on were the way to go. Somehow when i bought my frac i just didnt carry that info over, although my DSLR didnt seem to mind too much.
I'll take some new flats asap and update how i get on!