This advice may come a little late but it's good to know.
The two directories ~/.kde and ~/.pt are in fact hidden from normal view. This is true of all files and directories which start with a <dot>. They usually contain your settings and other configuration type stuff. There is usually one for just about every application you use.
To make them viewable:
In Konqueror click on the View menu and select Show Hidden Files.
On the command line add the all switch to the ls command i.e.
(that's LS in lower case)
You should now be able to locate those directories.
Like I said this may be too late. Have you still got a working system?
I have a similar problem. After installing an application I left disc one of the Mandrake 9.2 install cd-rom in the drive and rebooted. Before I could stop it I was into a fresh install. I was able to quit out of the install and I don't think any changes were made to the configuration but I can't be sure. It was either that or the application install which caused the problem.
Lots of items missing from the K Start menu. Mainly KDE and Mandrake Configuration stuff.
=STOP THE PRESS=
I think I have found a fix.
Open Mandrake Control Center. From the command line type
or from the K Start menu >Configuration >Configure your Computer.
In MCC click on System, then MenuDrake.
Choose System Menu from the box.
Then from the File menu >Reload System Menu. Fixed!
I hope this works for you too.