I do not know why its giving you the problem. Before we can help you, you have to answer some questions. What type of a external drive is it? Is it a USB, SCSI, or SATA? Did you check that the modules are loaded like sd_mod, usb-storage, scsi_mod. Did you check if either uhci, ohci, usb-uhci, or usb-ohci is loaded. What type of filesystem Knoppix mounted your FAT32 drive and SUSE drive. You should be able to use vfat for FAT32 and whatever filesystem you use for SUSE (I think it is ext3 by default). Try posting what dmesg says.
What runlevel are you in. You can go to the console be hitting CTL+ALT+F2 if you are in GUI (CTL+ALT+F5) or load up a xconsole program like xterm or konsole. If you want to use GUI filemanager, you can use mc in the console. If you copy files from your external drive to a directory that you do not have permission to access in a GUI filemanager like Konqueror or Nautilus, you are going to have problems. By going into the console or in a gui console with Knoppix you will be as root, so you can do anything to your hard drives.
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