You have one light that can be controlled from two switches at different ends of the room - it works fine.
You have another light that is always on and does not obey the switch - you have an unconnected wire but do not say just where the wire is.
If this Yellow + red sleeve wire is at the ceiling rose of the light that fails to work there's a good chance that you have wired this always-on light to permanent live rather than to switched live - Check the switch that fails to work the light - does it have a Yellow wire? If so it's switched live for the non working light.
Ceiling lights NEVER connect to permanent live - only to switched live - so you can turn them on and off.
Good luck...take care...
Peccavi
November 2009