In the Ultracontroller design, DONE does not go High when in SelectMAP mode.
The -g Persist:YES option in BitGEN must be used. In SelectMAP mode in the Ultracontroller, the bitstream is first loaded immediately followed by the ELF. If Persist is set to Yes, the pins used for SelectMAP mode are prohibited for use as user I/O. Otherwise, the configuration pins are released as I/Os right after the bitstream is loaded and the ELF file will not be loaded, which in turn causes DONE to stay Low. For more information about the Persist option, please refer to the section on BitGEN in the Software Manuals.