It appears that this was a bug in perl-5.6.0 that caused this to fail, but it was fixed in time for 5.6.1. Checking other versions I have here, it gives the expected answer:

  zen% perl -we 'printf "<%4.4d>\n", "42a"'
  Argument "42a" isn't numeric in printf at -e line 1.
  <0042>
  zen%
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for all versions in qw/ 5.004 5.004_05 5.005_03 5.6.1 5.8.* /, and the wrong answer:

  zen% /opt/perl-5.6.0/bin/perl -we 'printf "<%4.4d>\n", "42a"'
  Argument "42a" isn't numeric in printf at -e line 1.
  <0000>
  zen%
[download]

only for 5.6.0.

Hugo