I am currently a senior systems engineer at Nokia, and I can say without reservation that we face this problem also, identifying specific versions of software (binaries as well as sources). Binaries can change, even if the source does not, if for example the compiler is updated, or associated libraries. This is especially problematic when the libraries are (as is often the case) dynamically-linked shared libraries.
This is not my experience at all. In the Binary Analysis Tool I use fingerprinting using string constants, function names, variable names, and so on, and I can reliably tell versions of binaries apart (granted: the information has to be in my database). This is absolutely no problem at all.
