F28069U: Memory corruption?

Hello Community,
I posted this first here. got no reply and hence posting again in this forum.

I encountered a problem while testing a functionality. Following are the details:
1. after some troubleshooting, I found out that when 2 unsigned short global variables are removed from the build, the functionality works
2. So I focussed on stack overflow and memory corruption
3. I tested for stack overflow with traditional method of initializing stack with known value and running the system until
   the functionality of interested is executed. But I saw that stack was well within the limit
4. I tried removing other variables of same size from different files, but no use
5. even stranger was this -
    a. hex file that didn't work was loaded; as expected, that feature wouldn't work
    b. now I removed those two variables from the file; feature started working
    c. now I keep those two variables back; feature works even now!!
    d. I then deleted the workspace (.metadata) and reloaded the hex; feature stopped working!!
6. so I thought it could be workspace corruption and changed the file name, created new file. Nothing worked.

I am now clueless about how to debug this.
Does any one have better idea?

CCS - 4.2.4.00033

CGT - 6.0.2 (changing to 6.0.6 didn't help)


(let me know what other information is needed)

thank you,
Vishwanatha