The bad bags leaked phosphates, if I recall corretly. Skibop, do you have a phosphate test kit?
Let me make sure I understand you - the new setup was there for a week, and THEN you started having problems? One thought is that it could be high ammonia. Have you checked it recently, or just when you set up the new tank? You lost a lot of your good bacteria when switching out your old gravel. Just because eco is wet doesn't mean it's cycled. How long was your filter unplugged? Did you rinse it out really good when you did the change? Did you use tap water with chlorine, or that was kinda hot?
Now for the obvious questions, bear with me and don't be offended (I have to ask!)
For your 50% water changes, you used dechlorinator (assuming city tap)? You matched temperatures? No new meds? No house cleaners or other fumes in the air (bug bombs, carpets steam cleaned, etc.)? Did you have any lotion or soap on your hands when you messed with the tank? IS YOUR HEATER WORKING PROPERLY?
Test for ammonia (and phosphate if you have the test), double check that it isn't high. Ease up on the 50% water changes, no more than one every 3 days since they are potentially stressful and you haven't nailed down the problem yet. If you have city water, call your water company and make sure they haven't futz'd with the water lately. My local water company will occasionally do a high concentration chlorine flush before they switch back to chloramines and that likes to wreak havoc on my setups if I don't realize it beforehand.
EDIT: I'm also a Nebraska native! My family hails from Omaha