Eclipse Remote Run Plugin Issue

I did entire set-up as per documentation on Eclipse-Kepler. Subversive setup is working and I am ble to do check-in, checkout from the IDE.
On invoking remote run from IDE, the plugin analyses entire workspace and at the end shows message "No suitable modified files found for Remote Run."
This happens when local history shows multiple versions. Did anyone face similar issue? if yes then how to resolve it?