Well, MIME::Base64 has definitely changed - and the change has been only half-implemented. From perl-5.8.0 onwards (I think), MIME::Base64 has been part of core perl so re-compiling perl, as suggested by the admins, would fix the problem.
Another way to fix this particular problem would be to simply rebuild and reinstall MIME::Base64 (from CPAN source). But if there are a large number of other core perl modules that have been similarly affected then rebuilding perl might be the better option.