Some thoughts on this.

1. I would definitely recommend you get a support ticket open to get official response
2. I think the key to this is the following
   1. PnliteServer=http://xxx/Citrix/xxx/PNAgent/config.xml Storefront=yes ReconnectAtLogon=2 ReconnectFromButton=0
   2. With ReconnectatLogon=2, the device will autoconnect to any active and disconnected sessions when the device logs on.  
   3. Since it appears you are not logging off of the users session prior to changing the display settings, when the settings are set a re-auth is sent to Storefront which reconnects applications. 
3. Try this
   1. Logoff the session in ThinOS prior to changing display settings
      1. Does it auto connect to the users desktop?
   2. Change the INI to ReconnectatLogon=0
      1. reboot endpoint
      2. Login, repeat your test while staying logged in and see if it autoconnects
      3. My gut tells me it still will, because technically you are still logged into the thin client, and when you change display settings the receiver client sends the updated endpoint display settings to storefront, (but I could also see that it does not autoconnect)

Thanks