then the problem may be related to unconnected macro pins on the schematic.
The XEPLD 5.2/6.0 software does not tie unconnected pins to VCC or GND, nor does it stop with an error if unconnected CE or LOAD pins are encountered. It just gives a warning that the pin is unconnected and may create incorrect logic.
Library macros with mode pins (like the CE of a flip flop or the LOAD of a counter) are implemented with muxes in front of flip flops. The mode pins are the select lines on the mux. If one of the select lines of the MUX is left unconnected then the mux is reduced to an OR gate. This logic is usually incorrect.
Macro input pins should not be left unconnected in XC7000 schematics, especially LOAD or CE pins. If these pins are not used in the design, they should be connected to VCC or GND on the schematic.