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What causes the differences between these two section allocation maps?

Other Parts Discussed in Thread: MSP-EXP430FR5739, MSP430WARE

How can I  correct the section allocation map?  How does it get populated?  I've detected some differences in the section allocation maps between two files (attached).

1680.MSP-EXP430FR5739_UserExperience.zip

The two files are from two different projects.  Both have the same C code.  Project 123 works.  Project MSP-EXP430FR5739_UserExperience does not.  I could not find any project settings that can account for this difference in Code Composer Studio.  I discovered that the interrupt labels are missing and the stack is missing from project MSP-EXP430FR5739_UserExperience. 

If you want to recreate the problem here is my setup:

Code Example imported through Code Composer Studio resource explorer from MSP430Ware (single click):
C:\TI\ccsv5\ccs_base\msp430\MSP430ware_1_30_00_15\examples\boards\MSP-EXP430FR5739\MSP-EXP430FR5739 User Experience
Code Composer Studio Version: 5.3.0.00090 (used for both projects; the one that works, and the one that does not)
Hardware: MSP-EXP430FR5739

In order to create project 123, I just started a new Code Composer Studio project and copied the contents from the example above.