New changes were made to the bootini package in order to avoid the boot.ini file being rewritten every time a update is required.
The new changes are available here and were thankfully provided by mad_ady on the forums.
The board will use boot.ini to boot.
User made changes should be done to boot.ini.default
After changes are made to boot.ini.default run sudo bootini command to write your changes to boot.ini
Changes made to boot.ini will be lost when the package is upgraded.