.htaccess file clears itself when plugin activated

I recently changed my theme, and updated all of my plugins. After I made the switch, I had a fatal error, which we resolved. I have gotten back to stability, however, I am unable to re-activate the W3Total cache plugin. When I do, my site freezes, and the .htaccess file clears itself. I then have to go through a step or two to fix the problem. We discovered this after a day of fatal error.

So, I’d like to completely uninstall W3TC and re-install it. So the question is, how? Please advise.

Thanks

http://wordpress.org/extend/plugins/w3-total-cache/