BF707 having issues booting from SPI flash

I have made software that runs fine in the debug mode with the emulator (ICE1000).

Before it was starting from spi flash as well. After some (I think) minor changes ( changed a two divider values , one went from 4 to 8 and the other one from 80 to 120) it is still working in debug mode, but does not start from the spi flash any more. When I undo the modification it works again.

I have seen an earlier post related to the BF706 with a simulair issue. There the fix seems to be:

Build Settings > Tool Setting tab > Linker section, I un-checked "Individually map functions and data items" for General and "Eliminate unused object" for Elimination.

I tried this as well, but these items were already unchecked. In that post (is closed by now) they also mentioned a DND mode, to check the status. I have no clue what the DND mode is. I could not find it an explanation either.

I am using CCES 2.5. I have my own designed board. Also using emulator ICE1000.

Processor BF707.

Does any one has any suggestion/ idea.