Just tested my first Leonardo (R3) on Win7 x64 and ran into similar issues described above. Looking ad the Device Manager it seems that the problem might have to do with the fact that when reset occurs it takes a few seconds for Windows to update the driver to the new COM port. By that time the bootloader sequence expires and Windows re-loads the driver again. If I keep pressing the reset button during upload sequence the Arduino IDE successfully programs the board, but only after quite a few tries.
In short, I think the bootloader and/or reset sequence needs some adjustment to work reliably in Windows. I am surprised these issues haven’t been resolved on the board shipping now. I’ll likely be programming it via ICSP which is to say I don’t recommend this board for beginners.