OK, so it looks like this happens if you close Zotero while it's in full-screen mode. Prior to El Capitan, I don't think you could actually put Zotero into full-screen mode.
This is fixed in Zotero 4.0.28.8 for Mac, available now. If the auto-updater doesn't work for you, close Zotero and reinstall Zotero from the download page over your existing version.
(Reinstalling manually is almost never necessary or recommended, but the auto-updater in Zotero Standalone 4.0.28.6 for Mac is broken. We're working on ways to update people, but a manual installation of 4.0.28.8 is the quick fix. Your data won't be affected.)
Thanks for this, everyone! I had the same problem as well and never bothered to look into it - it's now fixed and happy to see that Zotero can now be maximized.
Hi, just reporting the same problem in El Capitan. The issue with auto updating BTW is that you can't force an update from within Zotero if you cannot get to the Zotero menu. I will try via the system update method.
Upgrade Storage
We'll work on a fix. In the meantime, deleting xulstore.json from your Zotero profile directory is the easiest workaround. See below for fix.
i'm on el cap using the desktop zotero app
(Reinstalling manually is almost never necessary or recommended, but the auto-updater in Zotero Standalone 4.0.28.6 for Mac is broken. We're working on ways to update people, but a manual installation of 4.0.28.8 is the quick fix. Your data won't be affected.)