I don't want to make any assumptions since I don't know how your system is setup and how you tried to reinstall.
Do you have Bootcamp setup?
Do you have FileVault2 enabled?
Are you using RAID?
What did you boot from to reinstall Lion? Did you use Command-R? Did you boot from your clone? Did you boot from a Lion Recovery Disk?
See if anything in this link provides answers.
Please provide step by step how you performed the erase and reinstall.
I have always used a USB thumb drive I created from the Lion Recovery Disk Assistant or one that I created with the Lion installer (InstallESD.dmg) restored to it to boot from. From there, I used Disk Utilities to erase the Macintosh HD and redownload/reinstall Lion.