Sounds about right. Right now there is no such thing as /wiki/index.php since you moved to /w/index.php. So /wiki/index.php is being treated as the page linked to by [[index.php]]. But the url for that is wrong since the proper key for that title is [[Index.php]] because by default [[foo]] and [[Foo]] are the same page. So MW is redirecting to the upper-case version at /wiki/Index.php. And the query is being discarded because the only thing inside it is the ?title=... (see what happends when you go to https://en.wikipedia.org/w/index.php?title=wikipedia). Ideally you'd have never used /wiki/index.php in the first place, but too it's late for that.
Now the path router I introduced that now handles short urls is fairly flexible. I haven't tested it but to experiment try adding this to your LocalSettings.php.
$wgHooks['WebRequestPathInfoRouter'] = function( $router ) { $router->addStrict( "/wiki/index.php", array( 'title' => false ) ); $router->add( "/wiki/index.php/$1" ); return true; };
The other, classic way to fix this of course would simply be a rewrite rule to 301 redirect all /wiki/index.php paths to /w/index.php.