See it in a guest session as well inc. no log out until 1.5 - 2 min elapsed.
Seen since orig. install on Nov. 6 using that day's image

As far as other bug - 
When I log in there are 2 unity-settings-daemon running, one for me, one for 
lightdm. However just time is needed until polkit, nm-applet, log out ect. 
start working.
This happens 100% of the time, not random.

Terminal output for 2 different attempts to open synaptic, (within 1 min
of log in. -

$ gtk-launch synaptic
doug@doug-Lenovo-IdeaPad-Y510P:~$ ==== AUTHENTICATING FOR 
com.ubuntu.pkexec.synaptic ===
Authentication is required to run the Synaptic Package Manager
Authenticating as: doug,,, (doug)
Password: 
** (process:2314): ERROR **: Got unexpected EOF while reading from controlling 
terminal.
Trace/breakpoint trap (core dumped)
polkit-agent-helper-1: pam_authenticate failed: Authentication failure

doug@doug-Lenovo-IdeaPad-Y510P:~$  synaptic-pkexec
==== AUTHENTICATING FOR com.ubuntu.pkexec.synaptic ===
Authentication is required to run the Synaptic Package Manager
Authenticating as: doug,,, (doug)
Password: 
polkit-agent-helper-1: error response to PolicyKit daemon: 
GDBus.Error:org.freedesktop.PolicyKit1.Error.Failed: No session for cookie
==== AUTHENTICATION FAILED ===
Error executing command as another user: Not authorized

Maybe try a new install or wait till mentioned bug fix lands?

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https://bugs.launchpad.net/bugs/1643711

Title:
  Some autostart .desktops are needlessly? being delayed for 1-2 min
  after login

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