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