If it's the one indicated by Kenichi Watanabe then it came with OSX 10.2 Either the 10.3 (which from your description sounds like a retail version) or the 10.4 should boot the computer. If you have 10.4 on the drive you should not use 10.3 or earlier to repair the drive. If you have 10.3 on the drive you can use the 10.3 or 10.4 disc to repair the drive.
Only use Mac OS X 10.4-compatible disk utilities with Mac OS X 10.4 volumes - http://support.apple.com/kb/HT2648
You can use Disk Utility in Mac OS X 10.3.9—and only Mac OS X 10.3.9—to check or repair a Mac OS X 10.4 volume (Disk Utility version 10.4.4 v145.7). Don't use an earlier version of Disk Utility, such as when started from a Mac OS X 10.3.0 disc.
I would try starting the computer in Safe Mode by holding down the shift key. This runs a repair feature similar to disk utility and also puts the computer into a reduced function mode. Then use Disk Utility to verify the drive. You may find that the issue is gone because either Safe Mode booting has cured it or because there were too many other things running when you did you other verify and a spurious error from an active drive was seen as a directory error.
Mac OS X: Starting up in Safe Mode - http://support.apple.com/kb/HT1455
What is Safe Boot, Safe Mode? (Mac OS X) - http://support.apple.com/kb/HT1564
Safe Boot takes longer than normal startup - http://support.apple.com/kb/TS1884
Mac OS X 10.4, 10.5 - Computer shuts down during Safe Boot - http://support.apple.com/kb/TA24054
Safe boot mode runs a directory check command similar to that used by Disk Utility's repair. In OSX 10.4 and later it ignores some stored information (cache) that is normally read that speeds up the boot process, and it moves some caches to the trash. It also uses only System fonts and disables all Startup Items, third party items, and any Login Items. Networking and some video components may also be disabled.
=Cloning And Backup Tools=
A bootable clone is an exact copy of your drive which is capable of booting your computer. Making a copy of your computer which is capable of actually starting the computer requires special copying procedures which simply dragging files in Finder won't achieve. Some people just back up data files but if you have problems you have to reinstall all your operating system and all your applications. With a bootable clone you just start up from the backup drive and clone back everything. Note, PPC generation Macs require Firewire connections to boot from an external drive.
To clone one hard drive to another hard drive you can use:
CarbonCopy Cloner - http://www.bombich.com/software/ccc.html (donationware)
SuperDuper - http://www.shirt-pocket.com/SuperDuper/SuperDuperDescription.html (shareware)
IBackup - http://www.grapefruit.ch/iBackup/index.html (free)
The Restore function of Disk Utility included in OS X. Kappy's directions - http://discussions.apple.com/message.jspa?messageID=8799711
Tri-Backup (commercial) - http://www.tri-edre.com/english/tribackup.html(commercial)
Silverkeeper - http://www.lacie.com/silverkeeper/ (free) - version 2 has some issues (references: http://www.macintouch.com/readerreports/backup/index.html#d12jan2009, and http://www.macintouch.com/readerreports/backup/index.html#d13jan2009) and it is recommended Tiger users stick with 1.1.4. Silverkeeper is no longer supported starting with OSX 10.7
Kappy's Backup Software Recommendations - http://discussions.apple.com/message.jspa?messageID=9065665 and https://discussions.apple.com/thread/3236992?answerId=15838096022#15838096022
Overview of Mac OS X Backup Programs - http://8help.osu.edu/1247.html