I thought I knew how to do this, but have remained confused for some time now. This old house has the bath lights and existing GFCI duplex outlet on the same circuit. I enlarged the duplex to a quad and installed a Cooper FD60MWC timer. I then put another duplex box below, and installed a second GFCI outlet, tying together the white wires from the timer and the new outlet, and running the black wires through the timer. This seemed to work. At least it did for a moment......

 

Try sketching a schematic, and posting. It will probably help you straighten out what you're doing to yourself too.