Sleep baby sleep
The day's on the run
The wind in the trees
Is talking in tongues
If your heart is torn
I don't wonder why
If the night is long
The biblical phrase “talking in tongues” is used in Acts 2:4: 
 “And they were all filled with the Holy Spirit and began to talk in tongues”. 
 It means to talk in different languages which were unknown to the speaker before. In the context of Cohen’s songs it means that the wind in the trees can talk to people now or animals or other plants but later the mouse and the cat resp. the wind and the tree both speak in tongues and thus can’t understand each other.
Lullaby