I have KDS v3.0.0 with KDSK 1.2.0 installed on my environment. I created a simple projeck for the FRDM-KL43Z demo board. This project has MQX (full) and some GPIO functionality enabled to control the LEDs on the board. A simple task is created to blink the LEDs on the board with the OSA_TimeDelay set to 100ms. Everything is built using Processor Expert to generate the source code.
This project runs on the debugger (USB Multilink Embedded OSBDM/OSJTAG - USB Port) fine until I attempt to add the fsl_hwtimer peripheral driver. The HW Timer period is set to 1000uS, everything else on the Processor Expert configuration settings for the HW Timer peripheral is not changed from defaults. The new code is generated using the 'Generate' button and recompiled for the project. The debugger is launched with a breakpoint set in the Blink LED task as before. Running the debugger appears to work fine and hits the breakpoint in the Blink LED task. Running the debugger again never returns back to the Blink LED task nor doesn't stop at the breakpoint. After pausing the debugger, it is running in the Idle task only. The Main task and Blink LED tasks are not running.
I verified this by removing the fsl_hwtimer from the Components list in Processor Expert tab, rebuild, recompile, and debug then running to see that the breakpoint set in the Blink LED task is hitting every time after running.