Features stuck in "default" mode even if settings changed

Issue Summary

I have two sites (dev and live) both are completely same; same code base same data in database (mirror site)
on one site (win), half of my features are in "override" which is expected due to changes I've made in views, rules, image styles etc. on the other site (linux) I have only couple of "overrides" and most of the features appears as "default" which is obviously wrong.

I tried to uninstall all features and reinstall them.
I guess I don't really understand how features find changes, can someone explain or link to the right document
Thanks