I encountered this problem last week as well and thought it was related to the fact that when I first created the project, I didn't set the compiler option and that it was set to Keil by default. I've gotten the project to build w/o this file but when I change some of the settings in PE and then "Generate Processor Expert Code", startup_ARM_CC.c gets added back to the generated source code. This is true even though I have changed the compiler option to IAR since then.
The workaround proposed by Jack Blather, above, doesn't seem to work for me because I don't see a Startup section on the build options tab of the processor (MK64FN1M0VLQ12 if it matters).
Before I start on the unpleasant task of recreating my project (I've got ~25 components defined) I'd like to make sure that there is no easier way to get around the problem using an existing project? Also, is there anything that needs to be done between creating the bareboard PE project and adding the MQXlite component? And will this problem come back when more components are added?
Thanks,
James