Programs installed but not visible in application folder

Try this as a start:

Enable Finder to Show Invisible Files and Folders

Open the Terminal application in your Utilities folder. At the prompt enter or paste the following command line then press RETURN.

defaults write com.apple.finder AppleShowAllFiles TRUE

killall Finder

To turn off the display of invisible files and folders enter or paste the following command line and press RETURN.

defaults write com.apple.finder AppleShowAllFiles FALSE

killall Finder

Alternatively you can use one of the numerous third-party utilities such as TinkerTool or ShowHideInvisibleFiles - VersionTracker or MacUpdate.

Do both items. Sometimes simply setting the Finder to show invisible files then turning off the option will make those invisible applications reappear. Sometimes it doesn't work. In that case you can try the following:

1. Enable the Finder to display invisible files. Leave the Terminal active.

2. Enter the following command line in the Terminal

sudo chflags -R nohidden

Put a space after "nohidden", select all the invisible applications you could not see and drag the selection into the Terminal window. Press RETURN. You will be prompted for your admin password. Enter it. It will not be echoed. Press RETURN.

3. Disable the Finder's display of invisible files.

Are you sure you are looking in /Applications and not in your user/Applications.

I realize you said root folder, but a find usually doesn't find invisible files. So, while they may not be showing in the Finder, I'm just not sure they're 'hidden.'

I'd still give what Kappy suggested a try. It just seems strange.

try deleting the Finder preferences file - ~/Library/Preferences/com.apple.Finder.plist - and restarting the Finder (you can do that from the Force Quit panel if you type command-option-escape)