Don't use merge after setting up your textures.
Merge takes all the surfaces from each selected object and puts them in a single object. This means that you will loose texture information from each individual object. (texture coordinates will remain but object specific properties will be lost - e.g. texture, texture repeat etc)
When you are building the model, and if you are using seperate texture files for each part, you should put surfaces that are going to use the same texture in the same object. Rather than fragment, which makes each surface an object, use cut-away-object (which puts all selected surfaces in a new single object).
Andy
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