Login issues on new Mercator updates

I'm having trouble pinning down exactly what's happening here, but it seems like when I update Mercator, I have troubles logging into sites in my multisite instance.

The only way to fix it seems to be to clear my cookies for that particular site. Then everything works again until the next Mercator update.

Caveats: I'm not positive it happens every time Mercator updates, but it has definitely happened multiple times, and I know it's Mercator because it has happened when the only thing changing in the deploy is Mercator.

Potentially uninformed theory: is something causing the user's cookies to be invalidated somehow?

I've been having this issue for a while now but have declined to report it because (as you can probably tell) I don't have a full understanding of exactly what's happening under-the-hood, but after experiencing it today I figured better to raise the issue and see if it's something I'm doing wrong or a problem other people are noticing as well.

Thanks!