Folders randomly deleting themselves

I’ve had folders go missing on two different laptops--both on 10.4.x. The most recent missing folder was on my MacBook Pro. I clicked on my desktop icon on the left sidebar of the Finder window and got an error message stating that the folder was missing. I searched for files I knew were inside but to no avail. Both times this happened the folders were in the sidebar. I rebooted my computer and I was able to click on the desktop icon and was able to get to the desktop but all the files were gone.
The last time this happened it was to a work folder inside my documents folder. And before you ask YES I’m sure I didn’t delete it.
Any ideas?
MBP 1.83 GHz Core Duo   Mac OS X (10.4.7)   + Mac Mini, PB 1.67 GHz

Just a little more info. When I search for a specific file I know should be there it will show up in the search with the correct file path at the bottom. But if I control-click and say open enclosing folder it will open a blank window.

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