Whenever I restart my OctoPi (Version 1.3.12) server, it does not automatically re-connect to my Ender 3 even though I have that option checked. I have to open my OctoPrint web server and click the "Connect" button, and it connects perfectly fine. Why won't it automatically reconnect to my Ender 3 after server startup like the option says?
Because you didn’t include logs.
Er... No, that’s actually the answer to why I can’t be more helpful 
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Looking at your octoprint log, it seems like you have two versions of The Spaghetti Detective installed. The beta version is no longer working and should probably be removed. You also have both The Spaghetti Detective and OctoPrint Anywhere installed. These have a known conflict, and OctoPrint Anywhere is being deprecated so I would remove it. I don't know if this fixes the auto connection issue, but won't hurt either.
You have both the Port and the Baudrate set to "Auto". You could try to switch to a non-auto setting. To see what port and baudrate to choose, re-open the Connection pane once you are connected, and note the port and baudrate that are shown (but now disabled). Then disconnect from the printer, and reselect those values. Before pressing "Connect", select the "Save connection settings" checkbox for good meassure.
Just changing the settings from Auto to the specific settings worked for me. I noted the settings, disconnected, set the settings to static values rather than Auto, connected fine, rebooted OctoPi for good measure, when it came back up it was auto-reconnected. Thank you for your help! Too bad it won't auto-reconnect using Auto settings. ¯_(ツ)_/¯