I'm sorry to insist but I still think there is something wrong with the function kmeans. For instance, let's try the same small example:
dados<-matrix(c(-1,0,2,2.5,7,9,0,3,0,6,1,4),6,2)
I will choose observations 3 and 4 for initial centers and just one iteration. The results are
A<-kmeans(dados,dados[c(3,4),],1)
A
$cluster
[1] 1 1 1 1 2 2
$centers
[,1] [,2]
1 0.875 2.75
2 8.000 2.50
$withinss
[1] 38.9375 6.5000
$size
[1] 4 2
If I do it by hand, after one iteration, the results are
$cluster
[1] 1 2 1 2 1 2
So I think that something is wrong with the function kmeans; probably the initial centers given
by the user are not being taken into account.