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This has been asked here before by @fizzgigg but unanswered.
Solution is simple when you change two lines of the plugin code. Lines 157-158 of the file “multisite-site-index.php” must be changed to:
'orderby' => 'domain',
'order' => 'ASC',AI suggested to use order by “blogname” but that did not work in my case, “domain” works great.
(Valid for version 1.1 of the plugin. Disadvantage: Will be overwritten when plugin is updated…)