I recently logged into my website and got the "a security update is available for your site" message. In this case, I needed to upgrade from 6.9 to 6.10.

I have a couple of upgrades under my belt, so I downloaded the tarball and started the process of upgrading Drupal. Everything ran without an error and after finishing up the update, I was kicked out to my administration page. But, the page said "a security update is available for your site." Huh, what? I just updated?!?

I figured there was a glitch with the update and ran it again. Same response. Then I thought it was a permissions issue - nope. That wasn't it.

My next step was to a
grep -r '6\.9' *
on the system modules directory with not one hit. And, ran a
grep -r '6.\10' *
on the system modules directory and every module's *.info file replied back that it was 6.10. I was stuck for days on this, but then I hit the issue. I happened to run the greps in the /sites/all/modules/ directory and I got a whole mess of hits. 6.9 all on system module files.

Apparently, someone had dropped a set of system modules in the /sites/all/modules directory by accident. And, they had been read into the systems table. So how did I recover? I did the following steps and it worked for me, but make sure you back up your files and and database so that you can get back to a safe position.

1. Put my site into garland theme (and defaulted my admin them back to default).
2. I looked and found the system modules that were the offending modules. In my case they were in a directory /sites/all/modules/ubercart/modules/ .
3. I deleted the offending files.
4. I went into phpmyadmin and went into the system table.
5. I exported (dumped) a copy of the system table in case I broke things
6. I searched for the offending path. In my case I searched the filename field for Ubercart to find all the paths that contained Ubercart.
7. I then manually corrected the filenames that were pointing to the offending files and pointed them to the /modules directory. I am not sure if you could delete the rows, so I just repointed them. So if it was /sites/all/modules/ubercart/modules/blocks/ to /modules/blocks/
8. Finally, I went back to the site and ran an update.php and then re-enabled my site's theme.

One caution. Do not add any other updates. Fix one thing at a time in this case (i.e. don't do a module update at the same time you are fixing this error). Do this in two steps.

Good luck!