Mike,
Okey dokey, results are in. The build of JBoss 3.2.4 / Tomcat 5 went fine and I replicated the problem you were seeing with debugging only working at the webroot level. The problem was caused by not using the Jasper 2 name mangling for JSP paths internally when performing source JSP / java mappings for JBoss. Long story short, it’s now fixed and debugging for JBoss 3.2.4 / Tomcat 5 will work beautifully in 2.7 GA.
Thanks for helping us get this support in place.