I've had a disappearing breakpoint problem with 2016a and now with 2016b. My startup.m doesn't use any relative paths, and my version of dbstop is the built-in function. This problem occurs spontaneously some number of hours after launching a new session, and it manifests in two ways:
1. Usually, the entire "breakpoint alley" vanishes, so there's nothing to click on to add a breakpoint. Only the line numbers remain in the left margin.
2. Sometimes, the converse occurs: The line numbers vanish and leave the breakpoint alley visible (and functional).
I can cure the problem temporarily by restarting my session, but that's a huge pain. Otherwise, the only mitigation I've found is to invoke Split Screen > Top/Bottom in the Editor context menu (right-clicking in the whitespace). In the resulting bottom pane, the view has all the normal adornments; the top pane remains afflicted.