This a really strange problem and I dunno how it exactly happens.
When I browse the contents of my USB drive (with PortableApps installed on it) from a normal user account, all folders and files are possible to be read from and written to except any thing under Documents folder. Now the more tricky part is even if I rename Documents folder to something else, Kubuntu gutsy does not let me remove files using the normal user account. I can sudo rm -f from a bash shell, but the command-line doesn't give me the convenience of choosing a random set of files using the mouse and I don't think I am going to enable the root account...for safety purposes.
Can anyone else try out with Kubuntu and/or other linux distros, to see where exactly the problem lies?