This has happened to me before... but not randomly. I think it happens when you edit the wall in some sort of way after linking the window, i.e. adding a mesh edit modifier and altering vertices or edges. This way you can loose linkage of the window. If this is your case, don't do it. The wall is not a very stable object, though I always use it, but only for simple wall geometry.
The "random" part is weird. Maybe u can give some more info on "random"?
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