Hi there,
I′m experiencing the same problems with my website. The .htaccess file keeps getting messed up, always a line split or extra characthers on the end of a sentence. This brings the entire site down.
I′ve contacted my webhosting services for help. In the meantime changed all passwords and users. I notice something – my .htaccess files keeps getting messed up everytime I update certain plugins like wordpress stats and Yak.
The solution so far – changed passwords and .htaccess permissions to 444. Let′s see…