I am facing strange problem with eclipse [Ganymede]. Once I added some breakpoints in my code and now even after I delete all those breakpoints, it appears again when I start th
Another solution
Eclipse -> Run -> Remove All Breakpoints - for removing all Breakpoints for all Time
Eclipse -> Run -> Skip All Breakpoints - for temporary remove breakpoints

Happened to me to. I think it's eclipse bug. I filed a bug for it, will update once there's progress on it.
You can go to debug prespective

and check or uncheck the desired breakpoint in the Breakpoints view

or show the view from the Window menu

Perhaps it helps to check the Breakpoints view (Ctrl+3, type 'breakpoints') and see if they are inactive only or something. There, you can also deactivate them all at once (strikeout button).