I just struugled through this problem. I fixed it by noticing that some modules I installed via sudo /usr/bin/cpan were installed with a umask 027, meaning that I, as "other", saw an inconsistent view of my Perl library space. When I fixed the permissions, the problem went away.
To address why perl loads the latest IO.pm but an older IO.so, assume the latest IO.so is mode r-xr-x--- (550). Perl will try to load the first readable IO.so it can find, which won't match the latest IO.pm
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