First let's understand that you are mounting your usb drive (/dev/uba1) at /usr. It is important to realize that /usr is just a directory and that you have chosen to ignore what is already there and use the namespace as a mount point for your external drive. In other words, you are not mounting the /usr directory, you are mounting your thumbdrive at /usr. This should clear up some confusion here.

Having said that, anything previously in the /usr directory will now be ignored. The _malformatted_ message you are receiving references the .desktop file, not your filesystem. There is much in the /usr directory that knoppix expects to find there. Find another mount point.