In my opinion your main problem in the flower room is the fact that you are using a 1000 watt Metal Halide and two 400 watt HPS. You have 1800 watts of poor light for large scale flowering, IMO. The 400 watters will not give you adequate penetration for big, dense buds, and the MH is probably the wrong spectrum for flowering. Replace all of those lights with two 600 watt HPS and you will see better results for less electrical costs, IMO.
I assume that you're using the MH to achieve some kind of full spectrum in flowering; this is a big waste of 1000 watts IMO. Instead, use a full-spectrum HPS bulb like the Hortilux if you want an extended spectrum in flowering.
Just my take based on what you've said so far...