HI,
The Mac Version can sort incoming messages or chats by Time or Manually (See View Menu > Sort Conversations).
The iOS version does not have this. The Newest chat which is also an iMessage in most cases is always at the top.
In the Mac version this appears to be only a sort for the conversations themselves (the order in which they appear in the left hand pane of the Main Messages window).
It does NOT appear to be a way to sort the iMessages or IMs within an iMessages Chat or a Buddy List chat.
The Mac version being Off and then turned On to sync conversations that had been held on an iPhone or iPad (or were in fact continuing) did seem to be the ones with the issue as the sync process and ongoing conversations seem to have different rules or priorities from the iMessages server causing new message to be out of place.
People do report that once the sync process has "caught up" Messages on the Mac can be restarted and the individual iMessages appear in the "right" order.
(I have not evidence of this due to my lack on Off line conversations as far as my Mac versions goes).
8:55 PM Sunday; February 17, 2013
Please, if posting Logs, do not post any Log info after the line "Binary Images for iChat"
iMac 2.5Ghz 5i 2011 (Mountain Lion 10.8.2)
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
"Limit the Logs to the Bits above Binary Images." No, Seriously