Keith,
The linking process will use the order of libraries and object files to determine which functions are pulled into the linking operation. And this step is done before the linker is ready to allocate the linked result to the memory map. Since your sections are being placed in a different order for the memory map allocation of the linked result, their order will not affect the function precedence that you are questioning. At least is how it would seem to behave in my understanding.
A more likely issue would be the distance between the function calls between the two sections or between these and other code sections. Trampolines should solve this issue, but it is possible that trampolines are not enabled for some of the object files. Check if trampolines are enabled. You can learn more about them in the Compiler User Guide or the Assembly Language Tools Reference Guide.
You may be using an older version of the compiler and tools. In that case, it would help to know exactly what tools you are using, and also the differences you find between your two linker .cmd files and your two linker .map files.
Regards,
RandyP