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Since upgrading Magento from 1.7 to 1.9 (and enabling MultiStore in the process), I can no longer see extensions in magento connect, yet they are enabled. These extensions were indeed installed using Magento Connect before the upgrade.
These Extensions are located in /app/code/community
I have tried clearing cache, and reindexed database to no avail
If you use the command line, I managed to fix this issue by running ./mage upgrade community extension_name, and went through all of my extensions doing this. They then were readded to the Connect Manager list, and the ./mage list-installed list. If you try to run ./mage install, it just says the files already exist, but upgrade seems to do the trick.
Just be prepared for the extensions actually to be upgraded, so make sure to test afterward!
When I had this issue it was because the files in this folder /var/package were not accessible by the web-server & php user.
So first step is make sure that the /var folder has the correct permissions per magento wiki
Also check the file "owner" is the web server i.e www-data / apache / nginx - depending on the web server / setup
In my situation, I use CentOS so in that directory I did ls- l to get a listing and see the owner & group of the files.
For example, I copied the files to my server using "ec2-user" but the web server user was "nginx", so all the installed modules in Magento Connect disappeared but still active and working, as soon as I changed the owner & group they reappeared.
"Magento Connect" shows only extensions that are installed through it. To see everything else, run ./mage sync at Magento home folder (make sure that mage script has execute permissions). This should synchronize manually installed and automatically installed extensions.
