After opening the project's summary.html file that I found in the _bsp folder, I saw the information about the reduced driver options and how it effects how the flash functions will not work if the reduced driver option is selected. Disabling that option fixed the issue I was seeing. However, it increased the program size by about 8K. So, now I am looking at how to select just the flash functions that are needed. Others had talked about putting defines into the alt_sys_init but that does not work or at least I could not get it to work.