I've got a tomcat webapp that uses a fingerprint reader. It works fine under Windows XP and Windows 7 if you double click on tomcat.exe. It doesn't work on Windows 7 if you run tomcat as a service.
I imagine that when run as a service the process doesn't have the required permissions to talk to the device. I've tried running it as an administrator and verified that it's doing so with Process Explorer.
What else should I check?