The title of this thread does not describe the problem, so could do with an edit. I will hold off doing that just yet until we see where this goes.
I assume you select Windows 7 from (dual-boot) grub menu and there is a 3 min delay before W7 comes up?
How do you know it is doing a disk check. Is anything displayed during this time.
Have you checked what is set to run at Startup on W7 is as expected?