My C drive was getting full, so I replaced it with a larger SSD disk using this procedure:

How to move Windows 7 to a larger hard disk

It was a success - everything works fine, EXCEPT if I do a complete reboot (cold or warm). Note that is not a notebook, but the same procedure of course works just fine all the same.

In the BIOS setup of the machine, I can move around using the keyboard etc., so it is there quite early in the process. However, when the machine boots to the W7 login screen, there is no mouse nor keyboard for 1-2 minutes. Then, suddenly, without any information on screen, they start working, and I can log in.

It "feels" like Windows is installing drivers or something, but I don't know how to check for that when I am staring at a login prompt with no working input devices.

If I put the machine to sleep, the devices are immediately available when it wakes up.

I have thought about deleting my USB root hubs in the device manager to force it to reinstall things, but I don't really know if this will have any effect, plus I am afraid it could have some negative consequences.

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Have you checked the Windows system event log? -> Execute eventvwr.msc – Robert Sep 8 '11 at 11:02
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