Version 1.5.5 is coming soon where we fixed the run start on end code problem.
I also fixed the 1.0.6 download link, thanks for the hint.
Regarding downgrade i can not say why it should be incompatible. I know 0.95 is but for 1.0.6 I'm not aware of a incompatible change. Anyhow something seems disturbing so I guess you would need to remove the host registry from $HOME/.mono/Software/Repetier-Host.