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TMS320F28069M: Program does not work after board reset

Part Number: TMS320F28069M
Other Parts Discussed in Thread: MOTORWARE

I have proj_lab09a from Motorware running on the board with some modifications for using flash to store user parameters. I'm doing the following:

1. Start debug session.

2. Make sure the motor can be controlled as expected.

3. Press the physical reset button on the board.

4. Click "restart" in the debugger.

5. Click "resume". Or keep clicking "step over" until the program stops.

Now at step 5 the program gets to this line: 

memCopy((uint16_t *)&RamfuncsLoadStart,(uint16_t *)&RamfuncsLoadEnd,(uint16_t *)&RamfuncsRunStart);

And then it just stops at some address with no debug information, where the disassembly shows ESTOP0.

This procedure worked when I tried resetting a clean proj_lab09a, but with no hardware changes with my code it crashes after reset. Before the reset I can also write to the flash and the correct data is correctly updated in the expected section, so the code related to flash itself does not seem to be the problem.

Any idea what could be causing it and how to resolve it?