Hi,
What "History" are you trying to remove ?
iMessages are stored in chat.db items in ~/Library/Messages and there are three that interact together.
Saved Chats (Set in the General Section of the Preferences > Save on Close) will Save the chat or conversation when the App is Quit, When the computer sleeps, if the computer is shut down with the App is open and when the Chat or conversation is dismissed from the list.
The chat.db items are the ones that are involved in "restoring" the iMessages "History" when you start a new chat with someone you have had contact with before.
The Saved Chats will work the same way for all saved chats, similar to the way the iMessages "History" works using the chat.db items.
(i.e. when you reconnect to the same person any Saved chat will be shown as well).
The items you seem to be removing are a bit over the top, but would seems to be aimed at clearing any sort of history to the app.
I am not aware of anywhere else that any history is held (I would not have emptied the Caches myself).
The Console log item is referring to Saved Chats in the subfolder called Archive within the Messages folder, deep within that Containers folder.
It would normally look for iMessages History via the Chat.db items (Or at least that is what I have always thought).
I am not sure what to suggest.
8:42 pm Tuesday; October 7, 2014
iMac 2.5Ghz i5 2011 (Mavericks 10.9)
G4/1GhzDual MDD (Leopard 10.5.8)
MacBookPro 2Gb (Snow Leopard 10.6.8)
Mac OS X (10.6.8),
Couple of iPhones and an iPad