I am not a big fan of projects with multiple batteries... in this case, you have 3. For instrumentation amps, I prefer the virtual ground methods.
The above being said, you need to break the problem down and analyze what is happening. Have you pulled the manufacturer's datasheet for the loadcell? Pulling the datasheet is job #1. If the manufacturer has given a basic circuit or test/validation circuit, try and use that as a starting point. You can also google on the loadcell part to see what others have done.
In this blog, a student is having trouble with the loadcell; http://electronics.stackexchange.com/questions/18669/how-to-wire-up-a-3-wire-load-cell-strain-gauge-and-an-amplifier
and the #4 answer is a good starting place for you. Get out your multimeter and take some readings. Do the readings make sense? Be methodical in your approach. From the manufacturer's datasheet, pull the no-load R-value of the cell. Use physical resistors in the bridge to substitute for the cell at no-load and at full load... are you getting the appropriate voltage measurements on your multimeter?
Unless you have stock in a 9V battery plant, try and simplify all of those power sources!