Hi,
We have almost same environment and same issue. It has become a nightmare since WordPress is now generating .htaccess file each 60 seconds all the time with same data.. but what make it worst is that from time to time it generate a malformed .htaccess file making our site offline with a pretty “error 500” and with a bunch of errors on logs.
What we have as a workaround right now to me make it continuously working is having .htaccess file with chmod 444 (not writable but readable).
Is interesting this problem since we have others sites with same setup with no issues and working perfectly.
I really hope it could be fixed on the code since has been impossible to us determine what is causing this.
–Rodrigo
