It should not make a difference AFAIK, the only problem with the Open Mode Warning is that booting takes longer as the device stops for a while to show up the warning.

I do belive however that the reason you cannot boot correctly is because you have some Aegis conflict, caused by signing keys not been created correctly for Open Mode (see this posting for example: http://talk.maemo.org/showpost.php?p...&postcount=656)

To get rid of the Open Mode warning and Aegis conflicts, you should do the following:

• back up your device, as this is going to erase data on it
• get the correct emmc.bin and firmware.bin for your device variant
• flash device to closed mode
• activate developer mode to get console
• give command disclaimer-cal remove View-openmode as user to get rid of the Open Mode Warning
• do the back-to-back closedmode/openmode flashing to get to open mode with correct Aegis keys created.
  (Note that is is not enough just to flash open mode directly, your keys have been already created and you will get the same Aegis problems as before...)
• set up your kernels
• set up your ubiboot config files
• flash ubiboot kernel