I agree that the best way to reset peripherals is to do it with an I/O pin on the microcontroller, but if you must do the reset as you have described, it is possible that your microcontroller is trying to access your peripherals before your peripherals have completed their reset. Try inserting a 100ms delay in code before accessing any devices. Also on the order of "did you plug it in" I might also add, are you sure your capacitor was inserted correctly (plus side to VCC)? If not, your reset circuit will not work predictably. If it was inserted backward, throw it out and use a new one as reversal destroys the cap. If none of the above work, try going to a 22uf cap or increasing the pull down to 20K or higher.

Ken