sometimes it depends on your optimization settings and other factors if breakpoints won't be recognized. Best way for us to reproduce your issue would be creation of a project archive as described here. Then post the archive here.
At first set the optimization level for the compiler from "Debug" to "none" in project -> Build options.
Keep in mind that a breakpoint stops the CPU, but no hardware as timers which will keep on generating interrupts that will be served when running again. So it might look like an interrupt handler never gets completed. when single stepping an area of code, keep interrupts disabled, there is an icon on Creator's menu bar for that.
I am getting message on output window Error 'SWD error NACK' received while attempting to read memory location 0X....etc
Are you using any power saving modes? Or really reading at locations where no memory is??