If you declare a variable in flash memory, like so:
#pragma PERSISTENT;
#pragma LOCATION(0x1800);
volatile MissionTimeType missionTime = 0;
When you try to view the variable by hovering, or in the expression window, you will get the wrong value.
It appears the IDE has the wrong address for the variable, as doing something like &missionTime, in this case, shows the wrong address (0x3000 in my case)
Using the latest and greatest version of CCS.