so you have the problem only with Elgg 2.3.9 but not any older version of Elgg

It was began early than 2.3.9. At least, 2.3.5 (as I remember).

I didn't pay attention to this issue because I thought that the reason was in the code, or on the server (we included memcache at that time). But now I see that I'm not alone ;)

possibly only with nginx?

I can't say that on nginx only. But on localhost with Apache I haven't this issue on Elgg 2.3.9. Unfortunately, I haven't a remote server with an Apache.

What does you plugin do exactly? What does it fix?

Just sets the access level in metadata ignoring changes made in #9069

3rd party plugins

Sure, I did it before (and always).

My opinion is a problem with the metadata' caching but I don't know where is it: server or database.

In our case, it happened when a 'Profile' plugin was disabled, used custom plugin without register_metadata_as_independent('user'); and we've upgraded Elgg to 2.x.

@RvR

I haven't done anything with the profile files, no mods anywhere on the site, and the plugins not working still.

register_metadata_as_independent('user'); i see this in the profile.php

i'v done a temp fix, which i can live with permanently if you don't find the problem with your plugin, i'v disabled the option boxes in profile edit

such a perfect platform i don't get why you even need these options as all the widgets and everything else can be set on private.

anyways thanks for the help, get back to me if/when it's fixed .... thank you ! :)