My best assumption right now is that when multiple Views contexts are put together, and one doesn't contain any Empty Text fields, this is triggered.
Changing line 32 of views_content/plugins/content_types/views_empty.inc from:
$block->content = $output['empty'];
$block->content = !empty($output['empty']) ? $output['empty'] : ''; fixes it; but I'm not aware of where-else the returned $block's data is used. Should this be