As others have said, double check your settings; while most auto setup/room correction programs are fairly accurate these days, they aren't always perfect and it is always advisable to double check things like speaker distances, levels and delays to ensure that no gross errors occurred when the program ran. Also confirm basic settings like speaker assignment, crossover for the sub, etc.
Is the graphic equalizer you are referring to a standalone component or a setting in the menu system of the AVR? If it's a separate component, that may well be causing your problems since the room correction software in the AVR likely includes EQ adjustments, and if that is indeed the case, they may simply be clashing with one another. Lastly, check your connections to make sure that nothing has come loose, and confirm cable directionality and polarity are both correct. If none of that helps, you may have a bad amp.