I was hoping that I could blame it on something other than the size of the speakers but oh well never mind. I guess when I tried the 6x9 and didn't have a problem I should have stopped kidding myself.
I have already set the high pass filter to 78hz on the HU though this is not ideal as a. it obviously removes all the low stuff and b. it filters the frequencies sent down the Sub preout as well
meaning I have to set the boost on the sub amp to 6db or 12db
Best solution I am thinking is to bypass the wiring from the headunit and run the front and rear components directly from a 4 channel amp (using the front and rear preouts of the HU) that way I can set the highpass filters on the amp and just use the HU to adjust the EQ etc - avoiding the problem with the sub preout too.