I think the issue in training has been fixed with adding array.layout = "rowmajor" in the training function of the R script.
There is still a warning in the predict function as from the log below, but not sure how to add the same code to the predict function.
Anyone has any idea ?

Thanks

log:
[27312] <2> ExecuteCode: in >>> Y <- neural.predict(2,X)
[27312] <2> ExecuteCode: out <<< arning message:
[27312] In mx.model.select.layout.predict(X, model) :
[27312] Auto detect layout of input matrix, use rowmajor..


neural.train = function(model,XY)
{
X <- data.matrix(XY[,-ncol(XY)])
Y <- XY[,ncol(XY)]
Y <- ifelse(Y > 0,1,0)
Models[[model]] <<- mx.mlp(X,Y,
hidden_node = c(60),
out_node = 2,
activation = "sigmoid",
out_activation = "softmax",
num.round = 10,
array.batch.size = 40,
learning.rate = 0.02,
momentum = 1.5,
eval.metric = mx.metric.accuracy,
array.layout = "rowmajor")
}