I’m getting an identical problem to this, after a while (not been able to determine exact sequence yet!) the breakpoints just get ignored.
One way around it was to close eclipse, re-open, build & deploy app (on tomcat 6) again then try again – this worked once but not after, as samula says “the scripts do not reload and are not available in the inspector”
any ideas on this? – this was the reason I bought the Pro version but I may have to try FireFox debugger
thanks
harry