I searched but did not see this mentioned anywhere. I noticed a couple of issues running multiple ATV 3's with PlexConnect.
They have the latest firmware 5.3 and PlexConnect build as of late last week.
The settings do not seem to stay with the ATV. If I change ATV (Bedroom) to show movies as "grid" then ATV (Office) settings change to show movies as "List". Also with the clock, if I change ATV (Bedroom) to 12-hour view then ATV (Office) clock changes to 24-hour setting.
Not sure if this is a limitation of the software at this point but thought I would point it out.