OK,
Lets try to sort out the semantics again
The App is called Messages.
It is effectivley iChat +
In setting it up you need an Apple ID to Register with the iMessages Servers
This then gets listed as an "Account" in the Messages Menu > Preferences > Accounts
Your Messages may then pick up on any iChat style Buddy list/Accounts you had prior to Mountain Lion and these will be in the list as well.
There will also be a Bonjour Option (everyone gets Bonjour)
If you have two "Accounts" in the list listed as iMessages there has been an error.
The iMessage Account only appears in the Preference > Accounts list and the Messages Menu > Accounts sub item (where it will be ticked in Logged in)
IF....
The iCloud ID is the one you used for iMessages and you also have an AIM Account you will only see the AIM list in the Window Menu > CMD + 1 (Buddies) Unless the Bonjour Account is also Active/Enabled or you have other "Buddy List" accounts that are Enabled and logged in.
Your 3) is the bit that makes me think we are talking about an iChat Style "Aim" account and an Apple ID used as the iMessages registration
Pause ....... >>>>>>
OK Your iCloud Apple ID is also an Valid AIM Screen Name meaning it can also be Added as an "Account" in the Preferences via the + Button as a AIM account listing the EMail type name in full with the @Me.com bit as well.
Like What I have
Staying with this Pic and your 3) I presume you mean you are using the Account detail Button and then the Sign Out button on the next pane ?
Re 6) I have this file in Mountain Lion
I can only Presume it has not been created yet as the Apple ID in question has not been Registered.
Can you use this Apple ID on the iPhone or an iPad in Messages (In iOS version) ?
It may pay to remove the two .plists you do have (the first lists the Apple Server iMessages connects to and the second looks like a hold-over from Messages Beta)
If you have com.apple.IMAgent.plist then delete that as well.
Restart Messages
11:17 PM Tuesday; August 21, 2012
Please, if posting Logs, do not post any Log info after the line "Binary Images for iChat"
iMac 2.5Ghz 5i 2011 (Lion 10.7.2)
G4/1GhzDual MDD (Leopard 10.5.8)
MacBookPro 2Gb (Snow Leopard 10.6.8)
Mac OS X (10.6.8),
"Limit the Logs to the Bits above Binary Images." No, Seriously