use of NA's

Can someone please explain why this works: 

d<-c(0,2,3,2,0,3,4,0,0,0,0,0)
d.mat<-matrix(data=d,nrow=4,ncol=3,byrow=TRUE)
for(i in 1:length(d.mat[1,])){

+ d.mat[,i][d.mat[,i]==0]<-mean(d.mat[,i][d.mat[,i]>0])
+ }

Whereas: 

d<-c(0,2,3,2,0,3,4,0,0,0,0,0)
d.mat<-matrix(data=d,nrow=4,ncol=3,byrow=TRUE)
d.mat[d.mat==0]<-NA
for(i in 1:length(d.mat[1,])){

+ d.mat[,i][d.mat[,i]==NA]<-mean(d.mat[,i],na.rm=TRUE)
+ }
dosnt

Thanks
Tom