It's possible that the Pro Tools user might have reseated or moved the Digi 001 PCI card to different slots in the CPU without removing the device from the Device Manager in Windows. Without removing the Digi 001 from the Device Manager and either reseating or moving the 001 PCI card in the CPU, multiple Digi 001 devices will show up in the Device Manager in "Safe Mode", possibly causing the Pro Tools application to not see the Digi hardware.
To get to "Safe Mode":

1) While computer is restarting hold down either the ctrl or F8 (depends on computer) key before the Windows Splash Screen appears.
2) Right-click on My Computer > Properties > Device Manager Tab.
3) Open Sound, video and game controller category.
4) Select each Digidesign 001 and remove one at a time.
5) Restart computer.
6) If Wave Driver is installed already, Windows will find the driver for the Digi 001 PCI card.
7) If the Wave Driver is not installed, install from Pro Tools CD, following "Getting Started Guide" page 19.