I'm using PEx with KSDK 1.3 on one project (yeah, I know, I'm working on moving off of it) and I discovered that it's not setting the MCG BLPE mode correctly. If you choose BLPE in a clock configuration, it comes out as kMcgModePBE - which doesn't exist on this part. The result is that when you try to switch to it, it looks up the appropriate transition from its matrix and gets the wrong answer, so it's perpetually stuck transitioning to FEI mode.
Here's a screenshot:
My fix for now is to disable the 'read only' option for the structure that it generates and override the setting myself:
clkLowPower.mcgConfig.mcg_mode = kMcgModeBLPE;
The clock manager is such a large chunk of code that I'm planning to ditch it as soon as I have time, so I'm not too worried about this but I thought I'd warn anyone else who might come across it.