Elementary debugging skills tell me that the problem is then with the few-line sub _perl_is_same. Which means that the string from Config->myconfig() isn't eq when dragged through print and qx.
Given that this is a little-seen problem and involves RedHat, my first guess would be a UTF problem. But I'm sure Ken would appreciate someone who has this distribution getting a dump of the two versions of the string involed. I'd find that trivial to do with the Perl debugger but one could also just insert some warn Dump Config->myconfig() or such code. (I don't have RedHat handy.)
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