well first, yes check that everything is placed as it should and that nothing is blocking flow in any way. Don't expect perfection though since the biocube is inherently flawed right out of the factory. check out this thread and its links.
http://www.nano-reef.com/forums/inde...owtopic=180788
The things I did on my 8g BC are as follows:
chamber 1: throw out the stock filter pad, put in a heater and bag of carbon (or any media you want). WIDENED the overflow between chambers 1 and 2 (do NOT make it deeper, just wider).
chamber 2: threw out the bioballs, removed the false bottom grate (use a coat hanger or something), replace top grate with a piece of eggcrate. Put in LR rubble and a piece of filter floss over the top grate.
chamber 3: threw out the sponge before the pump intake. Replace pump with a maxi-jet (i think yours fits an MJ1200... see the thread above)
intank: made a Y-shaped loc-line outlet (keeping the stock piece).
these small inexpensive mods all apply to the larger BC models as well. widening the overflow and getting rid of the stock filter cartridge will not only likely solve your current problem, but also allow you to replace the stock pump with the more powerful Maxi-jet. It really makes a difference.