You're confused about the function of the warnings pragma versus possible warning output from a particular module. The former controls diagnostic output and what not from Perl itself; the latter is controlled (usually) by some sort of option either passed to a constructor or the like (maybe setting a package varialbe). While it's conceivable for a module to look at $^W in order to enable or disable its diagnostics it's not common.

As for why reinstalling fixed, unless you're sure you installed the same versions it's possible you picked up a version that corrected a bug, or perhaps turned off whatever was causing the diagnostic you were seeing.