Pretty Permalinks issue and mod_rewrite is on

I just installed WordPress this evening and noticed something strange when I went to change the permalinks structure. On another WordPress-based site I’m hosting (using the same Web host), I see the following as the structures available to me…

https://mysite1.com/?p=123
https://mysite1.com/2009/08/07/sample-post/
https://mysite1.com/2009/08/sample-post/
https://mysite1.com/archives/123

So far, so good. I didn’t have to do anything special with this site. I set it up and saw this when I first logged into WordPress.

On my new site, I’m seeing this…

https://mysite2.com/?p=123
https://mysite2.com/index.php/2009/08/07/sample-post/
https://mysite2.com/index.php/2009/08/sample-post/
https://mysite2.com/index.php/archives/123

This doesn’t seem right. I am using the same .htaccess file for this site that I am using in the first site. I checked to see if mod_rewrite is active, and it is (for both).

I entered the following in the “Custom Structure” field, and it seems to be working, but why did I have to use a custom structure? Why is the second site different from the first? Could this have anything to do with the fact that Drupal is also running on the same site (I was using it until now for this site)? Or is my host just doing something strange with one server and not with the other (although, again, mod_rewrite is enabled on both).

Here’s the custom format: /%year%/%monthnum%/%day%/%postname%/

If that works, and it seems to work (no errors, and pages are displaying when I view them), why am I still seeing “index.php” in the example paths??

Thanks!