Are you using Lion? if so, you need to disable File Vault. This is a quote from a CNET article on this subject:
"In OS X Lion Apple implemented a new full-disk encryption technology called FileVault (or more appropriately "FileVault 2"), which first preboots the system to a log-in screen that requires you supply your password to unlock the drive before the system can boot. This configuration prevents the system from accepting a keyboard-based boot command like the Shift key and passing it to the operating system.
Apple has acknowledged this limitation with FileVault, and affirms that the only option for booting to Safe Mode if you have FileVault enabled in Lion is to first disable it in the Security (& Privacy) System Preferences. This may take a little while to do, but should not affect your data at all.
Do keep in mind that while this is the case for people using FileVault 2 in Lion, it is not the case for the first-generation FileVault technology in earlier versions of OS X."
You may have to first unlock this preference pane in order to turn it off.
Hope this helps!
I am still experiencing "Cool Runnin'" since the safe boot / reboot.