IR remotes control systems can be interferred with by other sources of IR.  For example, many plasma TVs emit enough IR to confuse other components.  In such a case, blocking the path of the offending IR from the IR eye in the non-responsive unit usually helps.  Note also that IR can be reflected from many surfaces, so if one component is emitting IR, you have to think of any paths that would bounce back,

So is your Linn Kairn able to see some part of the SKY box?  Glass doors in front of both units?  Is the problem actually your TV? Try turning it off before switching the SKY into standby.