Maybe @Tuicemen could post the path for WorkingDirectory and ExecStart.
In the meantime it looks like your init.d file may be corrupted. Since Raspbian Jessie, init.d is not used to launch a service. Systemd is now the standard way to launch a service for the reason that is so simple to create and maintain.
Below is a sample Systemd file to launch the Homegenie service. You will need to adjust the paths of WorkingDirectory and ExecStart to reflect where your copy of HG is installed. If you want to reply back before you start work on what I have set out below it might be easier for you.
What you need to do is stop the current init.d service, disable it and create a new HG service and launch it. You will name the new service as homegenie1.service
cd
sudo systemctl stop homegenie.service
sudo systemctl disable homegenie.service
Now you create the new service called homegenie1.service
cd
sudo nano /etc/systemd/system/homegenie1.service
Now copy/paste the following lines below adjusting the paths as I mentioned above as soon Mr T supplies them. As soon as you finish press ctrl-x keys followed by the key y and press return.
[Unit]
Description=Homegenie Server
After=network.target
[Service]
WorkingDirectory=/home/pi/homegenie
ExecStart=/usr/bin/mono /home/pi/homegenie/HomeGenie.exe --log
Restart=always
[Install]
WantedBy=multi-user.target
Now you need to enable the new service you just created and start it.
cd
sudo systemctl enable homegenie1.service
sudo systemctl start homegenie1.service
To check your service is running type
sudo systemctl status homegenie1.service
Could you screen cap the output of the last command and post it.