Sorry about that purpler. I can confirm the same behaviour, although I wouldn’t have expected it.
Seems the main modx rewrite is getting re-processed, and this new rule comes into play because it’s a request for index.php
In any case, the following qualifier will solve this particular problem, and hopefully not introduce any other problems. Please test various scenarios before deciding to rely on it.
RewriteCond %{QUERY_STRING} ^$
RewriteRule ^index\.php$ / [R=301,L]