Your machine is new enough not to have shipped with any ISA cards (or slots, probably), so I am assuming that your modem is a Winmodem, and is a PCI card.
If you post the make and model of your SCSI card, I'll take a look at that, but I am going to assume it must also be a PCI card.
PCI cards plug into the newer small white expansion card slots. The far older ISA cards plug in to a longer black slot, usually located on the far end of the PCI card sockets. Modern machines no longer include the old, slow, and non plug-and-play ISA slots.
My guess is that the paperPort software commandeered the IRQ previously used by the modem, or hijacked the address range it was using for I/O operations, or both.
Try this...
From the device manager (Start->Control Panel->System->Device Manager), uninstall the modem. (Don't physically pull it, just uninstall it's driver.)
Re-boot and let Windows find the modem again. When it discovers it again, it will assign it resources. These will be different from the originals which were hijacked. If my hypothesis on the IRQ and I/O switch were correct, your modem should now work. If not, no harm will be done.
If that fails, you'll need to have someone take a look at what happened and back it out.
Were the SCSI card drivers part of the PaperPort install disk you ran? If not, I can't see that installing the app first would be a good idea. It won't have an interface to bind to.
Let me know what happens.
You might want to use the Device Manager to take a look at assigned IRQs and see if you are full up, and determine from the list whether IRQ sharing is working if it is needed.
