There are profound differences between 5.6.0 and 5.8.0 that involve reading text from files (and these differences can cause unexpected problems on at least on some versions of Linux, possibly other OS's as well). Also, some "features" of 5.8.0 have since been "modified" -- the current stable release is 5.8.4 -- so that there are fewer bothersome differences in behavior relative to 5.6.0 (and earlier versions). For that matter, some of those Linux versions may have been updated to avoid some problems as well (I don't know).

That's all very vague, but as crabbdean has pointed out, so is your question. You must at least be able to make time to tell us in detail what you mean when you say "the script fails to read a config file correctly." Does it give an error message (and if so, what's the message)? Does it report no errors but end up with unexpected data?

While you're at it, it would be relevant (if you can spare a few more seconds) to say what OS type/version you're on, and indicate whether there is any non-ASCII data in the config file.