Hi Pat,
althought this might be better for the msp430 forum let me see if I can clarify for you.
This will depend on where you put the code that initialized the variables.
1 - If your msp supports it, and you put this initialization code in the boot strap loader (msp430 BSL) then they will get initialized every boot
2 - If you initialize them using your code, then they will get initialized any time that piece of code is run. So this depends on where/how you implement this.
Does this help? There are many useful examples and application notes on both the msp430 BSL and writing to flash.
Best Regards,
Lisa