Incomplete pathnames

I used the release of 1.5 to get a fresh start on my blog. I deleted the earlier version and did an install rather than an upgrade. Most parts work, but I’m having problems with WP inserting the file name into the comment & category links. You can see this at https://thefarmware.com/wordpress/index.php. For example, the url for a comment is https://thefarmware.com/wordpress/p=1#comments, it should read …/index.phpp=1#comments. I’m using the default theme and haven’t monkeyed with anything yet. I also noted that I have to specify the “index.php” in my blog url or I get a 404. I use other php scripts on my site and don’t have to include the “index” in the url, so I don’t believe its an os problem. Any suggestions of where to look would be appreciated.