This is a known issue. After the recent update, some users are being routed to the Agents Window on startup instead of the Editor Window. Since the Agents Window opens without your previous workspace context, your font size, sidebar layout, and open files don’t carry over.
To get back to your normal workflow:
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From the Agents Window, press Shift+Ctrl+N (or go to File > Open Editor Window) to open the Editor Window
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Close the Agents Window
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On the next launch, Cursor should remember to open the Editor Window
Alternatively, you can launch from the command line with cursor . --classic to skip the Agents Window entirely.
Regarding the “Open Agents Window on startup” setting disappearing after you toggled it off — this is a bug we’re aware of. The workaround above should keep you in the Editor Window going forward regardless.
You may also find this related thread helpful, where other users have shared additional workarounds: Set editor as default window