CI 3 input post not working when removed index.php

R=301 means an external redirect, that is requested by the server via a 301 status code ...

When that happens with a POST request, the client (browser) should ask you before making the redirect, but most (if not all) browsers will automatically do it and change it to a GET request.

There may be other issues with your rewrite rules, but this one is surely a problem - don't ever make an external redirect unless you want to redirect the client to a completely different site.