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Paul, I think you may be expecting a bit to much. You have to remember you only have 7.5 minutes of colour data to work with.
I would be inclined to say your main problems are Focus/collimation. Even with the OSC M42 requires quite a lot more exposure to fill the folds in the nebulosity with colour and detail.
This being one of the hardest targets to capture and process correctly I would suggest you persevere on something a little easier like M20 until you find your feet with LRGB.
Colour balance can also be a bit of a pain when using filters and Don Goldman has a good tutorial on his site about calibrating your colour filters with G2V stars. It's worth a look.
It is a huge learning curve when using filters and it will start to come with time. This is one of the reasons I went back to a OSC as I can easily get a reasonable image in one evening without having to spend hours and hours in photoshop. My work committments and patience ran out. No doubt with practice your end result will be better but try not to be to impatient and have everything right and in your favour, by this I mean focus , collimation and seeing. The sensitivity of the CCD will highlight any such problem.
I notice you are using CCD stack, which I have never used but being an image stacking program I expect it has provision to combine the LRGB images and set colour factors. This is where the G2V star calibration will help.
Good luck with it all.
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