OK, I just deleted the 'META-INF/' memeber before writing it back out and it works fine...the contents of META-INF/ are separate entries themselves so I don't lose anything...
So, the issue is with the lone directory member and both zip and jar complain. It looks like a problem with Archive::Zip to me. I'm happy because I love this module and I can use it without waiting for a fix!!!
Here is the code to create good and bad:
use Archive::Zip qw( :ERROR_CODES :CONSTANTS );
my $az_foo = Archive::Zip->new('foo.jar');
die 'write error' unless $az_foo->overwriteAs('bar_bad.jar') == AZ_OK;
my ( $meta_inf_member) = $az_foo->removeMember('META-INF/');
die unless $meta_inf_member;
die 'write error' unless $az_foo->overwriteAs('bar_good.jar') == AZ_OK