I know exactly what you mean. I have seen tile come up from Fiberock with 100% coverage on the tile and being able to see the contours from the shape of the surface of the Fiberock and even the ink from the printing on the surface of the Fiberock in the thin-set on the back of the tile, yet it still did not bond. The flip side is that I have also tried taking tiles up from Fiberock and having to destroy the substrate to get the tile up.
Personally, I really think that it is the mix that you use. I like Fiberock and use it quite often - usually either Fiberock or Ditra. I have found that some of the lower end thin-sets, particularly if you let them slake for too long in the pail, have a hard time bonding to the Fiberock. I know that you are supposed to be able to use an unmodified mix, but I simply feel more confident with a good quality modified thin-set that starts out a little on the wet side (not too wet of-course) knowing that if it gets too dry it may not bond as well to the Fiberock.
Installing it, we always use thin-set and staples. The Ditra trowel is a nice notch for this.
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J&D Tile