Another method to run stuff at the end of a program (or at the end of any scope) is to use one of AtExit, Guard or Scope::Guard, which are basically all objects that have a DESTROY method which does all the work:

sub at_exit {
    my ($callback) = @_;
    bless 'At::Exit', \$callback;
};

sub At::Exit::DESTROY {
    $_[0]->();
};
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But the difference to a normal END block is very small, and without more knowledge about how normal END blocks don't work for you, it's hard to know whether this solution will work better.