You mention having multiple projects, so I assume you have much experience with this IDE--if so, my past observations (of this and CodeWarrior) might not help you:
--You can only have so many breakpoints enabled in a project at once. (4 for the Kinetis K64, for example.) If you happen to enable more than 4 for the K64, the debugger can malfunction. The fix is to remove all breakpoints and re-set each.
--You cannot edit a source file above any breakpoints. If you do, the debugger can malfunction. The fix is to remove all breakpoints in that file at least and re-set each.
--If a breakpoint is set on a line without executable C code (such as a preprocessor statement), the debugger can malfunction. The fix is to remove all breakpoints and re-set each.
--Using the 'X All Debugging Sessions' buttons sometimes causes the debugger to act funny.
--Restarting the IDE has fixed debugging issues for me.
--Restarting the computer has fixed debugging issues for me.
--Re-powering the programming pod has fixed debugging issues for me.
--Re-powering the MCU has fixed debugging issues for me.
--Deleting/re-importing the project has fixed debugging issues for me.
--Deleting/restoring the Debug Launch Configuration has fixed debugging issues for me.
--Un/Checking the 'set breakpoint at "main"' setting in the Debug Launch Configuration has fixed debugging issues for me.