I do not think your use of an equalizer has caused any problems. I will explain the proper use of the source/direct button. This button's function is to monitor the output of a recorder connected to the record outputs of your amp. When this button is pressed on the sound going to the speakers comes direct from the "source" (cd, radio tuner, phonograph etc.) when in the off position you can monitor the recording of whatever source is being recorded via the tape deck. This switch must be off to record through the amps record outputs.
To test this, put a blank tape in the tape deck, choose the source as phono and place the dec in record/pause. With the source direct button pressed on you should hear a change in volume when moving the amp's volume knob only. When source direct is off you will be able to hear the output of the tape deck, so adjusting the tape deck's record level will also affect the volume coming out of the speakers. more record level in/ more level out.!
Below is copied from page 9 of your user operation manual for Marantz's explanation of the source/direct button.
best of wishes, Michael Mittelsdorf