Are you installing anything else after you get all the drivers loaded? Plugging in any external devices?
If so, what are you adding?
The disk check coming up and then causing issues with Windows makes me wonder if there is something hardware going on, potentially with the HDD.
I would recommend creating a Hirens Boot CD
and utilize some of the options available to attempt to resolve your issue. I would recommend running the HDD diagnostics either from your specific manufacturer (you didn't mention the brand) or one of the one's available.