I have similar problems.
At one Laptop (Lenovo T61, W7prof) all seems to be ok.
My second Laptop (T410, also W7) has problems. In device-manager all seems to be ok, but programming is only occasionally possible.
The funny thing: if i connect the leonardo at an USB-Hub, it seems to be better, but not ever...
I think there is a timing problem, eiter in bootloader or in avrdude. It seems, the time after resetting the leonardo is too short, so the changing of COM-Port will not be detected.