Auto generated htaccess file error?

I’ve had a problem for a while on my website, that I haven’t been able to find a root cause for.

Basically, every once in a while, .htaccess files are created in almost all folders on the site (Even folders unrelated to my wordpress installation).

Once a folder has this .htaccess file, the page no longer works. So once the problem happens, it takes down my whole site.

I have to go in to each folder and delete these mysteriously created files, in order to get it working again.

I’m suspicious that wordpress is creating the files, as it seems to occur after I delete spam comments in the admin panel. The issue isn’t repeatable every time though, so I can’t say it is wordpress doing it for sure.

Have anyone heard of something like this before? It is driving me nuts )