The issue seems to occur after updating to macOS Sierra.
After the update, the position of the tray icons changed (from what they had been before the update). Redragging them works, but they are reset to this certain position if the system is rebooted. This didn't seem to happen before upgrading to Sierra. (Either that or the icons are somehow always placed to the position I wanted whenever I install new applications, which is unlikely)
Is there a way to make the tray icon positions persist on reboot?
I have Bartender 2 installed, but I don't think it is causing the issue.