I have similar problem.
Inherently, breakpoints are working in that stepping, stepping over/into works, and (get this) "run to cursor" works!
Furthermore, if I go to Window->Debugging->Disassembly I can then set breakpoints in there and they work fine.
Problem exists with ICD3 or simulator.
Again, same OS same mplabx on two different computers - problem on one, but not on other.
(i.e. ironically on my main computer breakpoints are broken, but on an old slow laptop, they work great.)
And yes I know you have to set breakpoints only on code producing lines -- but no breakpoint works on any line. Really.
But for C lines (XC in default free mode) all breakpoints are broken.
I've had this problem for months - just upgraded to v3.50 to see if it helps, and no help.
Oh yeah, my project name and path contains nothing accept a-z A-Z 0-9 as user provided input.
Fresh install of latest mplab-x just today, all default settings for optimization etc.
Thanks very much,
post edited by JesseGordon - 2017/01/13 01:49:16