Another disappearing Messages problem

Mac OS 10.8.3
Messages 7.0.1
iOS 6.1.4
Every once in a while I will have a great number of Messages disappear from my Mac. This seems to only affect one conversation at a time and a few days or even a few weeks worth of conversations will disappear. For example, I have about 20 conversations open in Messages and one of those conversations is missing all the messages that were sent and received from and to all devices on Tuesday, whereas all the other conversations that had messages sent on Tuesday still have those messages present.
The missing portions of conversations are also missing from ~/library/messages/archive/, however all the messages are still present on my iPhone.
This is affecting:
Messages from iOS devices sent to my Mac/iPhone.
Messages from Macs sent to my Mac/iPhone.
Messages I sent from my iPhone to Macs/iOS devices.
Messages I sent from my Mac to Macs/iOS devices.
"Save history when conversations are closed" is checked, but I have never closed these conversations, so that doesn't seem to be relevant.
"Start New Conversations" from is set to the same email address on both my Mac and my iPhone.
I have recently reset PRAM for a different reason, and because this happens infrequently, I'm not sure I could link the two.
Any ideas?

HI,
I am going to thank you for your post.
It does make it clear that at least for some the non appearance of even disappearance of some of the iMessages is random.
I am beginning to think that this issue is unrelated to the issue the mixed up order of iMessages on the Mac version.
Although the chat.db (in the same folder as the Archives) is difficult to read in Quick Look or even Open With TextEdit - does it contain the "missing" iMessages ?
NOTE
I am not sure there is an answer to this at the present time but the extra info you have supplied does help.
8:49 PM Wednesday; May 29, 2013
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"Limit the Logs to the Bits above Binary Images."  No, Seriously

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