This problem is self inflicted but I don't know how to rectify it.
I went into the Service Menu > Linhes Configuration > Remotes and changed the Receiver from Hauppage to MCEUSB. The system reconfigured something and after I rebooted the remote did not work anymore. When I go to terminal and type IRW the remote buttons work fine, but I can't use it in Linhes, no menu navigation with UP or Down etc.

I went back in the Remote Menu and changed it back to Hauppage, rebooted, but still no go. The system has obviously changed something in the configuration. I am very new to Linux, so I hope someone is willing to help me out here. Thanks in advance.

Your remote is working. You need to tell lirc what the settings are.

You should have 2 files in your /etc/ directory called lircrc and lircd.conf.

Please upload the contents of those to files. The contents should be references to other files. Please upload those as well and I'll talk you through configuring them.

_________________
\\ENVY - LinHES 7.2
Athlon 64 4000+
2GB RAM
nVidia GeForce 8400GS
Hauppauge 350
MCP61 High Definition Audio
300GB

Thanks for your answer, I have been away for a few days but the problem is solved. The system updated the following file:

~/.mythtv/lircrc

to add: include /usr/MythVantage/templates/remotes etc etc.

These lines were added every time I changed the remote.
When I deleted all these lines except the first one it all worked again.
Thanks again