As Wilderness has explained, the .htaccess code you have was the default code placed on the website when the site was configured with Frontpage Extensions. Frontpage is a web authoring program that required a unique .htaccess file. In addition, Microsoft's Frontpage Extensions were required to be installed on the server for the website to be served to users.
As has been pointed out, Microsoft could not get the code for the .htaccess file correct. The suggestions offered rectify the errors.
Since you said you are not using Frontpage, I presume you are uploading changed and new pages via FTP. It is likely that much of the site has pages originally created with Frontpage, and these pages will likely not validate if run through the W3 Validator. One reason is that Microsoft used proprietary "webbots" to create special features.
FYI, one of the features of Frontpage was that it allowed you to upload pages directly from your desktop without the need of an FTP program.
Frontpage used a system of relative notation for links that allowed the webpage to be rendered on your desktop using your preferred browser. A normal link, e.g., www.example.com/directory/page.html might be coded as ../page.html depending on where you were on the directory tree. It appears to me that you may have a mix of Frontpage created pages and pages created by some other program or hand-coded. This may be why you are seeing 400 errors when you run the site through a sitemap generator.
When I dumped Frontpage as my site authoring tool, I notified my web hosting company to remove Frontpage Extensions. I had to go through each web page and remove any Microsoft webbots I was using and simultaneously repair all the links so that in the example given above the link reference now became /directory/page.html.
To create a sitemap using your sitemap generator may require you to go through the pages to remove any traces of Frontpage code and redo the links.
Make a backup of your site before making any changes. Any directory with a beginning underscore is a Frontpage directory which you will lose when your web hoster disables Frontpage Extensions (assuming that they are not already disabled).