The Parallel port is NOT a PCI slot. 'lpt' means 'line printer', ie, the parallel port line printer.
The computer is somewhat unable to scan the parallel port on its own; it needs the help of a userspace program, such as the front-end you are using to run the scanner. It also needs the parallel/serio kernel modules inserted into the kernel in order to read the port. Likely the computer doesn't recognize the scanner on boot, unless it is turned on, and turning it on later doesn't make the modules insert themselves.
I use a Mustek parallel flatbed scanner, and I have the following lines in my etc/rc.d/rc.local file:
Code:
modprobe parport_serial
modprobe parport_pc
modprobe parport
..and this causes the parallel port modules I need, to be inserted automatically on every bootup, whether the scanner is turned on or not. (Actually this scanner has no power switch; it is controlled via the parallel port completely). You can add these lines to your rc.local file, or a similar init script that gets run at bootup. Then the parallel port should be ready to go, all the time.
Does this help?