lionsilverwolf - I just wanted to thanks to you for posting this as I've run into the same problem recently with AR4 taking ages to merge 2 layers (about 15-20 mins each time).

It was driving me nuts but having read your post I moved an invisible group (which also had several other groups within it) above the two I wanted to merge and they now merge happily and at a suitable speed. What a relief! Thanks so much