Hi Jan,
an easy one first:
>>do people actually use Processor Expert for larger projects?
Yes, at least I do :-). Projects with > 50 components, with applications from <10k up to 512 KByte of code.
You can find a selection of example projects here: mcuoneclipse/Examples at master · GitHub
As for your actual problem: this indeed looks like a bug in Processor Expert around the PWM_LDD component.
I just filed this week end a ticket which looks similar to the issue you have. But I was able to generate code anyway.
I suggest you file a service request if not already done.
Anyway, if you are starting using Processor Expert, you probably should *not* start with the _LDD components. What I use is the much simpler to use PWM component:
Tutorial: PWM with Processor Expert | MCU on Eclipse
The other thing to be aware of: The timer channels on the Kinetis are unfortunately not as easy to use as on other Freescale processors (e.g. S08). As another point: if you are using a TPM module, the 'master' frequency of all channels need be the same: All the channels in a TPM need to use the same input clock and the same match register of the block (see the data sheet and block diagram of the TPM).
I'm using PWM with the LED's too, but using my own Processor Expert components:
http://mcuoneclipse.com/2012/12/29/pwm-and-shell-for-a-led/
This might be an option for you too (if it is about LED's). I have attached you a project you could use as a starting point.
But it is using my own Processor Expert components, so make sure you load the additional components first. See
Processor Expert Component *.PEupd Files on GitHub | MCU on Eclipse
If you build the attached project, connect to the FRDM-KL05Z with 38400 baud. Then you can change the PWM duty of each LED with the command line shell (see PWM and Shell for a LED | MCU on Eclipse).
I have attached the same project as on GitHub (mcuoneclipse/Examples/FRDM-KL05Z/KL05Z_FreeRTOS at master · GitHub), but with all the sources generated (It has the S19 file in it so you could try it out right away).
Last but not least: as with any new microcontroller, it always takes some time to learn new things. It is painful at the beginning, but will get much easier after a while. Keep going!
I hope this helps.