Mac Acting Erratically: Please help Safari iTunes Messing Up

Question

Okay I have an Apple PowerBook G4 running Mac OS 10.3.9 Panther (purchased late Nov 2003 was originally running 10.2.8 Jaguar) and up till a few days ago everything was running smoothly. That is until after I upgraded to QuickTime 7.1.2 and installed iTunes 6.0.5 when the problem started. Somehow my login.keychain for Safari got corrupted and I tried deleting original and making a new one.
Here's what has happened since then:
Any free media I have downloaded like videos or music off free sites (without Digital Rights Management) already still work. However, if I try downloading new stuff the new files don't work.
Since day before yesterday 4 times when I open iTunes it tells me my Library has been damaged. All my music files are still on my hard drive and are still playable but my iTunes Library file is corrupted -- how and why I don't know.
No music appears in my Library nor do any of my videos in .m4v format (iPod format) show up in my Library since then. I trash damaged file and re-import or select add to library and re-add all the media to my Library seems to work fine. I play them and most of them are playable. Even when Library works a few that played earlier have a skipping problem.
In Safari all my bookmarks got deleted -- I had to back, find the websites and re-add them -- fortunately when I closed Safari and re-launched the browser they remained saved the next time I closed and re-started the browser. However, third time (normally when something doesn't work twice they say third time's the charm) well the third time I opened Safari everything got deleted again.
My iTunes Library is acting erratically -- files I download don't work although files I already have are still playable usually except when my programs run across errors that didn't exist earlier.
I have Microsoft Office X 10.1.6 with the PowerPoint X and Excel X Security Updates, the Apple Security Updates 2006-002, 2006-003 and QuickTime 7.1.2 and iTunes 6.0.5.
When I originally downloaded and installed Security Update 2006-001 my Safari completely broke and would stop running and my Dock Menu dissappeared until restart but even then Safari stopped working. Could find no other solution than reinstalling OS X to return my Mac to pre Security Update 2006-001 levels. Not even Disk Utility solved the problem.
iTunes 6.0.2 also caused problems for me (I heard it caused problems on Windows also) the problem on my Mac was Disk Utility stopped working altogether. Fortunately, by deleting the game Chess from my Mac it fixed the problem. Today, I have Chess back on my computer because since my last OS reinstall I just updated my iTunes to 6.0.3 (I think) I now have iTunes 6.0.5 and have had no problems with Chess and iTunes or iTunes and another application like Chess preventing Disk Utility from working -- but now this problem I am describing where my Library erases itself regularly -- sometimes I restart iTunes and the new user wizard shows up and asks if I want iTunes to find my media and automatically add it to my Library when it does I say yes and it re-adds everything but somehow I have 2 files for every song on my computer and it re-imports (or imports) all my music, videos and podcasts back into my Library once and then re-imporitng it again
This time Safari is working but bookmarks are being erased and re-erased, iTunes is acting all screwy, files I download don't work when they should, I tried deleting and re-downloading a video I had saved on my hard drive (that I downloaded earlier) and the exact same file (no changes had been made to the file when it was re-uploaded) had errors playing when the download completed.
Fortunately, I had burned the video to a CD so I can re-copy it to my Mac and when I play it off the CD on my Mac or copy directly to Mac and play it works just fine.
Since downloading these updates cannot download anything anymore without errors when playing them.
If I downloaded same files earlier though they would have worked.
Only as a last resort would I do a clean reinstall of OS X -- thing is it would take a lot of work just to reinstall OS X, copy all my files I have backed up back to my hard drive, re-importing my music and artwork, re-installing Microsoft Office X and its updates, reinstalling some (but not all the latest ones if neccessary) of Apple's Security Updates, reupdating to Mac OS 10.3.9 to reinstall QuickTime 7.
I had like 283 files in my iTunes Library, including all my music, videos, podcasts etc.
Imagine how long it would take to get them all back in there; and I re-did it last night until it got erased again. Don't want to re-do it unless next time it stays permanently.
Just a note I also have Virex 7 on my Mac -- and it used to be a startup item but somehow it got disabled from starting up.
Also, I do have VLC Media Player but even that has been having problems with playing newly downloaded media files since I updated my QuickTime.
So the problem now is with my iTunes Library erasing itself continuously and even when its working sometimes refusing to play an entire track (it starts playing a song and then skips to the next one) I've checked my preferences and cross shading or whatever its called is unselected but sound checker is on.
Also the problem involves my Safari erasing bookmarks on its own as described above. Please help anyway you can!
As a last resort will do a clean reinstall, re-copy all my files back to my hard drive, reinstall my programs, re-update my Mac carefully etc.

Answer 1

Thanks for the help. I will take your advice and try running Disk Utility again. I have noticed sometimes when running Safari after quitting the application my defaults get changed -- that is my preferences go away. I have popup blocking and tabbed browing normally enabled by default it used to be if I enabled them as long as I didn't manually disable them that they would stay the same even after I quit and relaunch the browser, but now they get disabled when I quit and have to manually re-enable them again.
Also as noted bookmarks get deleted. Since the time I posted this thread I had at one time done a clean reinstall of OS X -- did it about 1-2 weeks ago. Not sure if videos I download on my Mac still have same problem but noticed if I download same videos on a PC that I used to download and play directly on my Mac that I could burn them to a CD or put them on a flash drive and transfer the file to Mac without any problems but downloading directly on Mac and then playing causes difficulty.
However, the same issue with Safari and iTunes has still been lingering for a while. I already have Mac OS 10.3.9 Combined Update installed should I try re-installing again? That would require me to reinstall OS X again and then update to 10.3.9. Or simply re-download and re-install 10.3.9 if possible over existing configuration so installing 10.3.9 over 10.3.9?
3 times out of 5 iTunes Music Library becomes damaged -- a few times I have tried since then deleting files in iTunes cache -- shouldn't become too big anyways -- otherwise it could become slow or something (good reason for cleaning Safari cache sometimes also) of course I wouldn't clean out the entire cache unless I had to or I thought that would fix the problem etc -- unless maybe it would even do a lot of good for resolving the problem.
I even tried trashing the damaged iTunes Library and the iTunes Music Library.xml file when the Library wasn't working.
If the problem re-occurs should I trash the iTunes preferences file(s) like iTunes.plist etc would help?