The fact that you have an attachments/ directory tells me that you are using the Attachments on the Filesystem plugin. Not that this makes any difference to the topic at hand; it is just a note.
I’m not sure why you are ending up with write-protected files. I haven’t heard of anyone running into this before. In fact, a search of this forum for the term protected only turns up one result… this post!
So I believe we’ve found your issue. You seem like you know your way around the Linux command line. As you actually have access to your own installation you are in a better position to figure out a solution. But if you want me to do some research and throw out a couple of suggestions, let me know!