When you boot OS X 10.6 to Safe Mode by holding the Shift key after hearing the boot chimes, you will see a gray progress bar appear at the bottom of the initial gray Apple screen. While this bar is showing the system will run various maintenance tasks such as checking the filesystem and clearing some caches, after which it will load into Safe Mode. This process should only happen if you intentionally boot into Safe Mode, but there may be instances in which you see it happen at each boot, even if no keys are held during bootup.
Persistent showing of this progress bar may mean either that there are problems with the system's start-up arguments, or that your system contains errors that it is trying to recover from at start-up.
There are a few things you can try in order to clear this problem, but before attempting to do so be sure your system is fully backed up. If this is happening because of an unrecoverable filesystem error, then you will need to format your drive.
Try clearing PRAM
PRAM stores start-up arguments that are passed to the kernel at boot. Generally these variables are blank, but if there is an error in the PRAM settings then resetting it may help. To reset the PRAM, reboot the system and immediately press the Option-Command-P-R keys after hearing the boot chimes. Hold them and let the system reset a couple of times, and then release them and allow the system to boot normally.
You can also perform a similar operation by manually setting the boot arguments to be blank. To do this, run the following command in the Terminal:
sudo nvram boot-args=""
One possibility (albeit remote) is that your keyboard could be sending the system the command to boot to Safe Mode. Try starting your system up with the keyboard unplugged to see if it boots normally, and if so then consider replacing your keyboard.
Verify or repair the disk
Boot to an alternative boot volume and use Disk Utility or, more preferably, a dedicated filesystem repair tool like DiskWarrior to run disk verification and repair routines on the boot drive.
Format the drive
If none of the previous options clear the problem, then formatting the drive should be a final step to take to clear the problem. Be sure you have a full and restorable backup of your boot drive, and then both repartition and format the drive using the OS X installation disc. Boot to the disc, choose your language, and choose Disk Utility from the Utilities menu. Then select the drive device (it will be the item above the "Macintosh HD" name--or whatever you have named your boot drive). Then go to the Partition tab, select "1 Partition" from the drop-down menu, and click Apply to rebuild the partition tables and format the drive.
After the drive is formatted, use Apple's restore utility (from the same menu) to restore a full Time Machine backup to the boot drive, or boot to your cloned drive and restore it to your internal boot volume.
A quick word of caution: If you have Boot Camp installed or have otherwise partitioned your main boot drive, then repartitioning the drive will destroy these secondary partitions. Be sure to back up your data on these partitions and prepare to set them up again after formatting the drive.