I regularly paint my Merbau decking. After my last coat, just 3 months ago, it has started to flake. It hasn’t done this before. Why is it happening now?
I assume you are using a deck stain not a paint. The stain has formed a film on the surface of the deck wood, hasn't penetrated into the wood. This is why it has peeled. Stains are designed to penetrate not form a film on the surface.
This type of deck wood must be sanded and then wiped down with acetone to open up its pores before staining. Penofin for hardwood is a great deck stain for Merbau.