This is most curious. URL path rewriting to allow clean urls (no ?q= in Drupal) work just fine on all the sites on the server except those that are accessed through the port that directs
I've checked out the rules in the sites-available configuration files and all of this is exactly the same.
Somewhere there must be port-specific rules that set up URL rewriting for the normal port 80 only?
I removed "Indexes" that followed Options and indented the Order allow etc commands, so that it looks identical to its live sibling, just a tad higher in the same file:
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