What was the problem with in-place Upgrade that made you decide on a Custom clean install instead? Describe any symptoms before and besides the one you desribed above.
Did you boot from the DVD to install Windows? Format the drive first?
Did the problem described begin AFTER you installed Windows Updates? If so:
Boot into the Windows 7 DVD, choose Repair my Computer on second screen, then in the Recovery Tools list, choose System Restore to restore the computer to before the Updates were installed.
If this works, then resintall the Updates one at a time with a System Restore point before each, until you find the problem Update. Take all the time you need.
If the problem is not related to Updates, then boot into the DVD and run Startup Repair 3 separate times as there might be multiple issues to fix.