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How to troubleshoot application without debugger?

I develop application for the C5505 based custom board (CCS 5.2, CSL 2.01, JTAG Blackhawk USB560-BP).

I experience very strange phenomenon. Application works 100% absolutely fine in debugger. However as soon as I burn the application image to flash it works only partially OK. Some features are OK and some are not. I can't blame flash or burning process since if something was wrong all app features wouldn't work at all.

My feeling is that when I run from flash some data remained uninitialized which causes this strange behavior. However when app run in debugger it initializes all data by default.

Any tips, ideas, comments how to troubleshoot application without debugger are welcome.

Thanks

P.S. I have 3 leds connected to board, so I tried to troubleshoot app without debugger with help of turning on/off leds. So far without any success.