Found this on their website for those like me who received version 6.1 deluxe
The following are known issues with PaperPort and PaperPort Deluxe 6.1 when installed on Windows 2000:
PaperPort print drivers are not installed.
The following dialog comes up when you attempt to run PaperPort: "This program does not run correctly on this version of Windows. To continue, click Run Program. To exit, click Cancel. For more information, click Details."
Users are not able to "Create a new link" in PaperPort.
Users are not able to use PaperPort when installed as an administrator.
Icons for NT Imaging and MS Paint do not show up on the Link bar.
Error message when attempting to use FormTyper.
PaperPort crashes after scanning a document.
CAUSE
PaperPort was released before Windows 2000. Therefore, it was not designed for use with it. The problems are the result of changes made to Windows 2000, which are not fully compatible with PaperPort.
SOLUTION
Click here to download a Windows 2000 update for PaperPort Deluxe 6.1. This update will provide solutions to the problems listed above with the exception of print drivers. For Windows 2000 print drivers it is necessary to upgrade to PaperPort Deluxe 7.0.
link