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TMS320F28069M: Running in debug mode as expected. When running stand alone sometimes doesn't move.

Part Number: TMS320F28069M

Tool/software:

I'm running an altered lab 13b type program where I'm using different ST_PosMove commands. 

I estimate the initial position of the rotor using hall sensors and estimating a QEP encoder value similar to the method explained here:

https://e2e.ti.com/support/microcontrollers/c2000-microcontrollers-group/c2000/f/c2000-microcontrollers-forum/411516/bldc-runs-backwards-when-using-a-qep-encoder-but-only-from-certain-motor-start-positions

This works great for in the debugger but when I try to run as standalone it won't move in certain initial positions. I already move all ISRs to RAM at start up and moved the constants and real time library to ram as well.

Anyone have any other suggestions?