I just purchased the program and gave it a shot. It is replacing my htaccess file. I basically had the same directives as what the program wrote except mine did have hot link protection and secure htaccess included and now it's gone.

Any ideas?

I have never seen that before Tom as it is specifically designed to append. The only thing that comes to mind is permissions.

I would suggest opening a support ticket and providing us FTP access at the same time so we can take a look at it closer.

The permissions for the htaccess file is 644 as it should be.

Anybody else experience this?

That is the same permissions that I have here. I just double checked with 2 of my hosting accounts we use for testing (Godaddy and 1&1), both have an existing htaccess file with information in there. When I configure WAM to protect a directory, it always appends our code to the file, preserving what was there.