I assume you mean the Microsoft Visual Studio debugger.
When I have goofy break point behavior, I start a debug session and open up the Debug Breakpoint window, then regardless of what shows or does not show for break points, click on the button with the big red X. Use that button - do not delete individually, nor not click X if it appears as if no break points are set. Then add back your break points. The X (IMHO) appears to remove the entire Breakpoints object as opposed to removing items from the Breakpoints (s stressed) object. Recreating the Breakpoints object seems to reinitialize something.
