Thanks all.
I think these are my options then...
1/ Seperate Mini Pro to control the RGB leds, and link it to the Mega via serial to select the mode/output I require.
2/ Bluetooth module instead of IR (serial). Make a bluetooth remote instead.
3/ Err
So, looking like option 1. I want to use a cheap IR remote and not have to make a bluetooth app for this thing.
I am having the occasional moment where the RGBs are doing some random twinkling effect, even though the first command is to clear the LEDS. Not figured that out yet.
If I run the RGB's off their own Mini Pro, then I can 'switch on' the Pro Mini when required.
Just makes programming a bit more of a pain that's all.
Thanks chaps. Learn something new each day and all that