Hi @Ale
First let me thank you for all the help!
I need to re-apply for the NDA to download that document since it is still not public right? At least I couldn't get it through your link.
Meanwhile I have tried your suggestions which were pretty similar to what I had already did. I will describe here the full procedure and attach the application for reproduction purposes.
Like I previously mentioned the application works fine using the Lauterbach.

As expected, LED D12 blinks:

Next steps following your suggestions:
1. Creating the IVT. My configuration:

RAM Start pointer:

RAM Entry pointer:

I pressed "Exported Image" and "Align" after filling the data.
2. Flashing the board. Configuration and steps:

Pressed "Test Connection" and then uploaded algorithm with success.

Then, download the app to the hyperflash:


3. Power cycling the board and changing RCON switches and J125/125 to boot from hyperflash.

RCON:

However, I keep not seeing D12 LED blinking with this method. Could the size of the application be a issue? Or what could be wrong?