It appears that Remote Desktop under WHS behaves much like Terminal Server 2003 as when I install software (Such as ActiveHome, TVersity or Titan Backup) it will often fault and crash if I try to start it up under a terminal session. The correct way to add programs in Terminal Server is to go through Add/Remove programs in control panel, but WHS does not seem to give the normal prompts (such as 'did the program install successfully after setup).
I installed VNC server (and manually added an exception to the Windows Firewall as it doesn't always prompt me for such under terminal mode) and rebooted. After reboot I can connect via VNC and all the above mentioned programs seem to work correctly.
For future program installs I will run them through the VNC session.