.htaccess file causing internal server error

I have recently been experiencing an “Internal Server Error” message and it appears to be the result of the .htaccess file not having a file extension. If I rename the file from .htaccess to .htaccess.bak the problem goes away for awhile then returns.

Any help figuring this out would be greatly appreciated. I am thinking it might be a plug-in. Is this something a plug-in would do? Or is it something more fundamental.

I am using WP 2.6 with the Thesis theme.