I've created a custom board using the 32u4 programmed with the Leonardo bootloader via the USBtinyISP and for some reason it will not reset on power up. I have a 10K pullup on the reset line but no 0.1uF cap to ground like on the 328P designs. Every 32u4 schematic I've seen has just a 10K pullup and a reset button to ground so I copied this layout.
I power up my board and nothing until I hit the reset button. Then it starts up properly. I'm guessing that a real Arduino Leonardo board probably resets properly on power up without hitting the reset button.
What's the power source? Your power source could be causing the chip to brown out on power up, disabling itself until reset.