Screwy Permalinks

I’m stumped and hoping a permalink expert can help me:

My website http://www.etny.net has a custom permalink structure: /index.php. I then use the “Custom Permalinks” plugin on all my pages. This works perfectly with the pages but does not work with the posts. In order to publish a post I have to click on the “get shortlink” button and copy from here (example = http://www.etny.net/?p=2048) the /?p=2048 portion and paste it into the permalink field. If I don’t do this, or if I enter my own permalink, the result is the same: The post will take me to the homepage. It will display fine in the archive, but the post itself will redirect. The category archive is http://www.etny.net/thedigitalfrontier.

Anybody see a solution? Thanks!