Files, Apps missing and re-appear after connecting to external drive

The problem:

I've had this very, very strange issue occurring over the past few days now where recently created files go missing or updated files revert back to earlier versions. It happens when I disconnect from my Time Machine external LaCie drive after backup. Even apps went missing and I had to reinstall them. It's like my machine is automatically reverted to two days earlier when I disconnect the external drive.

When it started:

The first time I experienced the problem was *after* I added my Macintosh HD (internal) drive as an exclusion to the Spotlight list of excluded drives/folders. I did this because my Mail app would not allow me to select "Entire Message" when searching mail folders. A popular thread told me that if I added and then removed my (internal) hard drive to/from Spotlight, that it would re-index it, thereby finding the mail files again allowing me to search the message bodies.

That's when the files and apps disappeared and/or reverted to previous versions. Again, the files reappear after I plug into the external Time Machine (LaCie) drive. But when I disconnect - they're gone! Other preferences have disappeared too - I've been prompted to re-enter serial #s I entered days prior for new software I added.

Machine: New MacBook Pro
OS X: Version 10.5.6
External Drive: LaCie 1TB

 

Update

I solved this issue. It appears to be a preferences issue. I used Disk Utility to verify and then rebuild my preferences which appears to have resolved the problem.

 

Correction

Thanks sickmacdoc - you're correct. I repaired my permissions - not preferences.