I've recently been noticing this.
It frequently seems to happen AFTER I create a new localization, and give it a unique name... it seems to "forget" what I've named it and reverts to the project name.
If that's not obnoxious enough, there are times when I've cleared out all of the points from a localization and saving it, and it still shows a number inside the little "house" icon, as though there were still points being used.
A bit confusing trying to determine which localization I was working on, and whether it's mistakenly still got points that it thinks it should be using "behind the scenes"... My typical solution is a Scorched Earth approach, where I delete the design data on any pages using that localization, set those pages back to the default or projected system, delete the confusing localization, and then start from scratch. Time consuming, unfortunately, but the only way I can guarantee to myself that something funny isn't going on...