Due to a loose comparison in inc/indexer.php, there is no differentiation in metakeys like 01 001 0001. Only the first tag makes the index, the rest is skipped.
I tracked it down to line 299 of inc/indexer.php
$id = array_search($val, $metawords);
$id = array_search($val, $metawords, TRUE);
The default is not strict:
mixed array_search ( mixed $needle , array $haystack [, bool $strict = false ] )
Which will result in the observed behavior.