The system is an MCF5235, CW 6.4.
However, we may have found out what is happening.
This project was started out on the eval board. I started out using an example from the operating system vendor - it seemed like the right idea at the time, and this was my first project using CodeWarrior.
We had figured out that the chip selects were not being set up, but we were not sure about the best way to add that initialization code.
A service request to Freescale brought up the issue of hwinit.c. While this code is in the project, it was called too late to make a difference. However, I went to look at it in the stationery example in:
C:\Program Files\Freescale\CodeWarrior for ColdFire V6.4\Stationery\ColdFire\CF_M5235EVB\C\CF_M5235EVB_C.mcp
In ROM-UART settings -> Linker - > ColdFire Linker -> Entry Point
you will then see exactly what is going on. The entry point is set to _asm_startmeup instead of _start. Do a search for _asm_startmeup and you will find it in "mcf523x_lo.s"
This contains the chip select initialization code that is effectively missing in my project. This generally went unnoticed because my project was derived out of the operating system example project instead of the CodeWarrior stationery project.