Sotware does not run on new XEM 3001.V2 boards

We purchased 5 new XEM 3001 v2 boards. The manufacture date is 01/09/07. We seem to be able to not run the code we were able to run on older XEM 3001 boards we had. We have five older boards and all five boards are able run the code. The manufacture date on those boards is
02/15/2005. All boards look identical from the outside.

We are running VHDL code compiled using XILINX 9.1 application version J30 and interfacing the board using a C++ graphical user interface made using Microsoft Visual C++. We are using your front panel dll. The code used Front Panel DLL that came with the FP 3.0.0 version. The newer boards came with a front panel version which was marked as 3.0.2

The problem we encounter is as follows.

I able to control specific pins of in the FPGA using the GUI. However, my state machines dont seem to work with the new board. For example, I can use a radio button on the GUI to set a pin on the FPGA but I cannot output a bit sequence that uses a state machine. The statemachines are controlled through the GUI. I can also output the clock.
Please advise.