Kevin,
[quote user="Kevin Taberski"] I have a new problem which appeared after I updated from CCS 5.3 to CCS 5.4. [/quote]
Did you do the update from within CCS or did you do a separate new install of CCS 5.4?
I can't think of anything that would cause the program to not run from Flash when power cycled, especially if all that changed was an update from 5.3 to 5.4.
The update process from within CCS has had a few glitches but I still wouldn't think that would cause this type of an issue.
One recommendation would be to try programming the part using a standalone programmer such as LM Flash programmer or Uniflash and see if that allows the program to run when power-cycled. That could help identify if the issue lies in the tools or somewhere else.