AFAIK the .classpath and .project files used by eclipse are kind of just meant to be guidelines (since for almost everything I've looked at in JBoss I've needed to make some minor modifications).
If I have understood you correctly, you should open the jbmail project properties in Eclipse and select the Libraries tab. Delete the JRE System Library and press the Add Library button. Select JRE System Library, and make sure you point to a 1.4.2 JRE (or create a new entry for JDK 1.4.2).
Hopefully that will solve your problem.
that's my bad --- should have documented it in file 'BUILDING.txt'. will do so right after posting this note.
i added a user library called 'JBOSS_LIBS' a while back which should be instantiated by each eclipse end-user locally. this library should include all the jboss jars (in $JBOSS_HOME) which are needed to build the jboss-mail project.
in eclipse 3.0, its under the Window/Preferences menu, and then under the Java/Build Path/User Libraries tree node.
there i defined a user library called 'JBOSS_LIBS' which includes all jars from $JBOSS_HOME/server/default/lib and $JBOSS_HOME/lib (substitute $JBOSS_HOME with an actual directory on your system)
this is the only way i know how to do this in an abstract and portable way (involves a tiny bit of work on every eclipse instance), and i bet there's an even better way to do it but unfortunately i'm an eclipse newbie and only use it occassionally. most of the time i use emacs/shell but often go to eclipse for some of its special features.