I have the same behaviour on my box. It has openSuSE and Karmic installed on different partitions and I have an usb hdd with ext2 FS on it. When I plug my usb hdd to my box with openSuSE loaded it seems to be OK: usb hdd partition correctly detected and got mounted. When Karmic is booted I have to mount that usb hdd manually.
I have the same behaviour on my box. It has openSuSE and Karmic installed on different partitions and I have an usb hdd with ext2 FS on it. When I plug my usb hdd to my box with openSuSE loaded it seems to be OK: usb hdd partition correctly detected and got mounted. When Karmic is booted I have to mount that usb hdd manually.