If you take a look at
perldoc perllexwarn you'll find that the warnings pragma is not exactly the same as setting
$^W. In particular, the pragma is scoped to the enclosing block. So if
$^W is getting set, you can be pretty sure that you need to search for an actual
$^W assignment, and not a
use warnings pragma.
You could use the perl debugger to find the offender. Or just grep your files and modules you use for $^W.
Also note that, if you don't need pre-5.6.0 compatability, then look at perldoc warnings and in particular warnings::register() which provides a good way of turning on and off your own warnings, giving finer control to the user of your module.
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