I'm pretty sure that CVSPlugin 1.6 didn't have this problem, but with 2.4 my URLs for ViewCVS contain the path portion of my CVSROOT.
For example:
Example base URL for ViewCVS (FreeBSD-CVSweb): http://cvs.somewhere.net//cgi-bin/cvsweb/
CVSROOT=username@host:/var/lib/cvs
Module being checked out: company/product/src
Resulting URL:
http://cvs.somewhere.net/cgi-bin/cvsweb/var/lib/cvs/company/product/src/Common/libs/widget/Widget.cc
Previously, the URL would have been:
http://cvs.somewhere.net/cgi-bin/cvsweb/company/product/src/Common/libs/widget/Widget.cc