Apparently, JSP files are added with -kb to CVS. I noticed this because my $Id$ strings weren’t being expanded, and confirmed it with cvs status.
I’m having a hard time imagining any reason why -kb would be necessary for JSP files, so I assume this is a bug.
I’m running 3.6.2 with Eclipse 3.0M3 on Debian Linux, using JDK 1.4.1 (actually a beta release of 1.4.1 from Blackdown). This is a fresh install of Eclipse, not an upgrade.