I have run accross a strange problem with plugins.

I decided to upgrade one of my sites recently to 3.08.  After running
the fix.php to update all of the files, I found that with the new
version of boltwire, the gui plugin no longer displayed the icons
above the edit box.  I tried a number of things including uninstalling
and reinstalling the gui plugin.  While trying this, I found that
plugins install no longer showed the list of plugins to install
(including ones that were already installed) - It showed that no
plugins were available even though the plugin's directory still had
the same php files (identical permissions) as before.

I created a new subdirectory did a fresh install of boltwire added the
gui plugin (which worked fine), added the new dropdown solution
(thanks to Dan and Linly which also worked).  Then I copied over all
of the files from the original pages directory and verified that
everything worked (after copying I noticed that everything had to be
reindexted but that worked fine too).

I verified that the plugins install list was populated correctly and
that the installed plugins worked like they should be.

Lastly I deleted the original boltwire directory and all of the field
content including the index.php file.  Then I copied all of the
content from the test subdirectory back to the parent directory.
Funny thing is, when I checked the plugins link - no plugins showed in
the list of "installable" plugins again.

I tried deleting and copying the files over several different ways
(ftp, rsync and cp) to preserve attributes but each time, I had the
same experience.

My question now is...  What can be causing the plugin list not to
populate after the site is moved to a new root directory or doing an
over write (upgrade) with ftp?
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