Binos,
Sorry to hear about your odd Bookmarks problem. When you do Apple-D, does it ask you to name the bookmark and ask where to put it? If not, you might need to repair your permissions:
1. Open Disk Utility (in Applications>Utilities)
2. Select your Hard Disk (should be the top one in the list)
3. Click "Verify Disk Permissions"
4. Click "Repair Disk Permissions"
5. Quit Disk Utility
Reparing Disk Permissions is the only kind of Disk maintenance needed on the Mac nowadays. You should do it when new software is installed, or maybe once a month, just to keep on top of things. It doesn't trash your system by having ikky permissions, but can create frustrating little things like you are experiencing.
Also, do you have all the latest software updates from Apple? The latest system is 10.4.7.
AppleMacster