I'm almost sure this issue never occurred to me with 4.3.

• Create some breakpoints before running the application
• When the debugger is initializing (while reading symbols), try to delete a breakpoint by clicking the sidebar or pressing F9.
• From this point on, you can't delete any breakpoint until a breakpoint is actually hit. The only way to delete breakpoints is by right-clicking the Breakpoints pane and choosing Delete All Breakpoints