I found this article when researching the issue you describe here named A flashing question mark appears when you start your Mac found http://support.apple.com/kb/ts1440.
Check the mouse and keyboard
This issue might occur if a mouse or trackpad button is pressed during startup. Make sure the button isn't pressed.
If the issue persists, shut down your Mac with its power button, disconnect any external mouse and keyboard, then turn on your Mac with its power button. If the flashing question mark issue persists, reconnect the keyboard and mouse.
If your Mac still starts to a flashing question mark, follow the steps below. If any step resolves the issue, you don't need to continue to the next one.
- Select your Mac OS X startup disk with Startup Manager by restarting and holding the Option key. After your Mac starts up, restart again to verify that the flashing question mark does not appear.
- If the issue persists, insert your Mac OS X installation disc. Be sure to either use the disc that came with your Mac, or, if you installed a later Mac OS X version from disc, use the newer disc.
MacBook Air note: On a MacBook Air, there are two options for starting up from Mac OS X media: Either connect a MacBook Air SuperDrive to the MacBook Air via the USB port and restart the computer, holding down the C key during startup, or use Remote Install Mac OS X to startup from a system software DVD that's located on a partner computer. Once started up from Mac OS X media, skip to step 3.
- Restart the computer, then hold the C key during startup.
- From the Utilities menu, choose Disk Utility. Don't click Continue.
- Select your Mac OS X disk (named "Macintosh HD" by default) in the left side of the Disk Utility window.
- Click the First Aid tab.
- Click Repair Disk to verify and repair any issues with your Mac OS X startup disk.
- After repairing the disk, try to start up normally.
Important: If Disk Utility finds issues it cannot repair, you may need to back up as much of your data as possible (or use Time Machine to back up to a different disk), then erase the disk and reinstall Mac OS X. You should back up important files and data before erasing a drive. Erasing deletes everything on the hard disk (including things on your desktop). Also, you can install Mac OS X onto an external disk, start from the external disk, and use Migration Assistant to transfer items from your usual internal Mac OS X startup disk to the external disk, then erase the internal disk and reinstall Mac OS X.
- If the issue persists, and Disk Utility didn't find any irreparable issues, quit Disk Utility, quit the Installer, select your disk when prompted, and restart.
- If the issue continues, reset PRAM. Note: After resetting PRAM, if the computer starts up normally, reselect the startup disk in the Startup Disk preferences.
- If none of these steps resolve the issue, start up from the Mac OS X Installation disc and reinstall Mac OS X.