In itunnel Browser or ifun
If you Click on the Root directory and then click on the \Applications directory you get an error
It tries to follow a sym link to \private\var\stash\Application.KJwGc1
But there is no such directory.
If I go to stash directory I see a directory called Applications.Qio6Qd
Which has all the apps.

Is this normal.
How do I go about fixing this.
Can I just Delete the root Applications directory and recreate a link pointing to the right directory.
Or does the right directory name keep changing ?

No, that's not normal. You can delete /Applications and create the link, in a terminal (or PuTTY) as root,
ln -s /var/stash/Applications.Qio6Qd /Applications

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iPhone 3GS / 3.1.2 JB (PwnageTool) / 04.26.08 carrier-locked, Carrier Logo Fixer / Cydia / 1000 posts on Hackint0sh

Installing Cydia programs on a phone that has no internet connection: read this.

Editing binary .plist, .strings, .nib and .xib files:
* on your computer: Windows tool / conversion website.
* on your iPhone: convert those files in a terminal with plutil (installed with Erica Utilities) or edit them with iFile (Cydia links).