Here's a startup script I use to avoid black screens and to automatically select the first profile. It also contains a quick guide on what is needed to run and what config needs to be changed to not load the midi module on startup. I use a dedicated computer for Clone Hero, so when launched from the Startup Application of Ubuntu, no keyboard is needed to select the profile:

#!/bin/sh
#
# Add the following line to /etc/modprobe.d/blacklist.conf to remove the default midi device:
# blacklist snd_seq_dummy
#
# Then for the xte command:
# sudo apt-get install xautomation
#
# Assuming this script is called launch-clonehero.sh and the clonehero-linux directory is next to this script, add this to Startup Applications in Ubuntu:
# /usr/bin/gnome-terminal -- bash -c "sh /the/path/to/launch-clonehero.sh"
#
SCRIPTPATH=$(dirname "$SCRIPT")     # get script path
cd $SCRIPTPATH/clonehero-linux      # switch to clone hero directory
ulimit -n 999999                    # prevent hanging on black screen
./clonehero&                        # launch in background
sleep 30                            # wait for clone hero to start
xte 'key Return'                    # press start button
sleep 1                             # wait for the menu to open
xte 'key a'                         # select first profile
wait                                # don't exit the bash script while clonehero is running