Sounds like a partition might be inaccessible for whatever reason. Tell your computer to boot from the optical drive and start the installation of Windows 7. Here you will be presented with some options related to your partitions. If everything looks right, just continue. If something is wrong, maybe that will shed some light on the issue.

In order to choose boot priority, you can in most situations just reboot your computer and press the F8 button while it's booting. If that doesn't work, enter your BIOS and set up the boot configuration in there.

If you've already done this, then your original post isn't clear enough about what has and hasn't been done.

edit: oh, I just realised you're probably using a Linux bootloader. That can very easily fuck with your Windows installation. That is probably what your computer is complaining about. I suggest you remove the Linux installation completely. It's useless anyway, since you have Windows 7.