If the old plist is overwritten, I would think there is only one plist. Yet when I search for "Bookmarks plist" I find a total list of 301 with different dates and different hours of the day. When I import different plists I find that the list of bookmarks in each plist is somewhat different. This seem to indicate that a new plist is created each time a bookmark is added or deleted.
I have never seen that. You have an error of some kind in your system and I would suggest you repair the hard drive as well as permissions, then run the 10.4.11 combo upodater again and reinstall Safari 4.0.3.
Repairing permissions is important, and should always be carried out both before and after any software installation or update.
Go to Disk Utility (this is in your Utilities Folder in your Application folder) and click on the icon of your hard disk (not the one with all the numbers).
In First Aid, click on Repair Permissions.
This only takes a minute or two in Tiger, but much longer in Later versions of OS X.
Background information here:
An article on troubleshooting Permissions can be found here:
If you were having any serious problems with your Mac you might as well complete the exercise by repairing your hard disk as well. You cannot do this from the same start-up disk. Reboot from your install disk (holding down the C key). Once it opens, select your language, and then go to Disk Utility from the Utilities menu. Select your hard disk as before and click Repair.
Once that is complete reboot again from your usual start-up disk.
More useful reading here:
Resolve startup issues and perform disk maintenance with Disk Utility and fsck
For a full description of how to resolve Disk, Permission and Cache Corruption, you should read this FAQ from the X Lab:
Apple's advice on general maintenance: