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Compiler/TMS320F28069M: __attribute__((ramfunc)) Problems loading functions into RAM

Part Number: TMS320F28069M
Other Parts Discussed in Thread: C2000WARE

Tool/software: TI C/C++ Compiler

I have been working on a project that is based on the InstaSPIN projects which uses the method for putting the ISR into RAM which looks like:

#pragma CODE_SECTION(somefxn, "ramfuncs")

// Copy fxns from flash to ram at startup
mem_copy(....)

and I'm trying to move away from that to the more straight-forward approach that is talked about here: http://processors.wiki.ti.com/index.php/Placing_functions_in_RAM . I can see in my .map file, that the functions are placed in the right place, also when I run the code and use a breakpoint in the debugger, I see that my ISR is being run, and the program counter shows the right address, but for some reason a lot of things suddenly start breaking. My eQEP module stops counting, I no longer get interrupts on my SCI interface(which is being run from flash) and I can't send information out of the SCI, I use a blocking write call and it happily allows me to write to the Tx buffer but nothing ever comes out the other end. Any ideas on what's going on here?