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Custom Boot-loader User Application

Other Parts Discussed in Thread: TMS320F28035

I have developed a custom CAN boot-loader for the TMS320F28035 but I have discovered that the user application which can be stored through it does not operate as expected. 

What i am finding is that certain variables (more specifically variables and structures within the TI library) seem to not be modifiable by the application code.  For example, the CpuTimer0.InterruptCount variable will not increment within the application.  My RAM is broken up into two sections starting at 0x8000 and 0x9000 each of length 0x1000.  When I export these ram locations for the stand-alone application and the boot-loaded application and then compare them in WinMerge (against their respect memory range), I find that there are big differences between the two.

For a custom boot-loader is it necessary to have the application manually copy the initialized sections from its application into RAM?  If so what is the best method of doing so? 

One additional detail that I noticed was that if I loaded my user applications symbols in place of the boot-loader symbols and then went to Target->Restart, my user application would run properly.  However, if I added the user application symbols to the boot-loader symbols it doesn't function properly.

If someone could illuminate how this works and how I can make my application run properly it would be greatly appreciated!