How do I change the boot mode on the SHARC Audio Module?

The ADSP-SC589 has multiple boots modes. JP1 jumper allows for three of the supported boot modes on the DSP, depending on jumper setting.

wiki.analog.com/.../main-board

When I send the code of the VirtualAnalog synth in RELEASE mode through the debugger it works perfectly, the Debugger goes pink, the yellow LEDs 10, 11 and 12 blink, and sound comes out and interacts with MIDI perfectly. I upload the code without the BOOT jumper and then I disconnect  the DEBUG connector, turn it off, put the jumper on the pins 1-2 (closest to the ethernet connector). When I turn it on it doesn't reboot. I have to upload the code again through the debugger for it to work. What is going on?