Custom keyboard shortcuts disappearing; more frequent in 10.4.7

I assign a good deal of keyboard shortcuts through the Keyboard preference pane. Very handy shortcuts like 'Zoom' to CommandShiftW, reassigning switch tab in Camino, and an iTunes 'Shuffle' shortcut to Command+S.
This is great, but periodically these shortcuts are lost when I return to the pref pane to add another shortcut. Once I load it up, none of my shortcuts appear, as if I had hit the 'Restore Defaults' button. It's hard to reproduce, but it's definitely very annoying, and has been occuring more often after I've updated to 10.4.7.
I know that these shortcuts are kept in .GlobalPreferences.plist and in the .plists of the respective applications, but I don't think I should have to backup these files and then overwrite to restore my settings.
Again, I don't see any definite triggers for this, but it does happen somewhat frequently. Does anybody else have this problem? Or perhaps some suggestions?
1.33 12" iBook G4 10.4.7   Mac OS X (10.4.6)  

You're welcome.
Will Techtool Deluxe (part of Applecare support) work
or is it only Techtool Pro 4.0.4?
I don't know. It would depend on what the problem actually is and on the capabilities of the utilities you have. As long as you don't use something that's not appropriate for your system, you can try it. There is no way for me to know whether you're going to be able to solve the problem by using a particular utility.
If I do have to do the zero and reinstall how do I
make copies of installed programs which came with my
computer but are not on the restore disks.
I don't understand. If they came with your computer, you should be able to reinstall them using the Mac OS X Install disks. The Install disks that came with my iMac G5 certainly include AppleWorks.
You can verify this by proceeding to reinstall the system without actually doing all the steps, just those necessary to be able to customize the installation and check that all the applications that came with your computer appear there as an option, then cancel the installation.
I am not talking about the
documents which I do have backed up.
Well, not sure what you mean by "documents", but if you're going to erase the disk, you should backup your entire home folder first, not just the documents. You're going to lose all your mail in particular if you don't backup the ~/Library/Mail folder before erasing the disk.

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