Update (6/14/13).-- I discovered one of the source of the unaccounted memory, which is accounted for in the activity monitor, I just overlooked it until I tried something. When you open the Apple App store app/window, it creates an "installd" daemon which tracks the apps and updates.
The problem is that daemon eats memory, like 500+ MB's in my case and it doesn't kill itself when you close the App store app/window, but sits there ready when if/when you open the app again. I don't know if you can kill it and it will safely recreate itself or not. I just rebooted after finishing up with updates to the App store.
I still haven't found the other 300-500 MB's when I open and close a lot of heavy use apps like Adobe's Creative Suite apps (eg. Photoshop, Dreamweaver, etc.). I can't find a daemon which is using the memory after closing the apps and running the purge command.
Original Post.-- I updated to OS-X 10.8.4 the day after is was available and have discovered something interesting I can't explain and no one on the Apple forums seem to either. After each update to OS-X I run some basic tests using the activity monitor and the memory allocations.
What I've learned, some of which is normal, but something isn't from previous versions of OS-X. After I reboot I open a terminal window, the Activity Monitor Window and the Console (log) window. I check the memory after running the purge command.
Ok. There didn't seem anything new there as for the size of memory allocated, eg wired, active inactive and used, which is that if I leave the Mac running the wired memory increases to a maximum of an additional 400-500 MegaBytes (MB's) which is normal as files increase.
But what is new is that the active memory starts off low, about 800-900 MB's, but over half a day to a full day, it increases by 400-500 MB's and this is after the purge command. Also, if I close all my open apps and run the purge command, the same thing happens, the active memory increases with no reason for where it's allocated.
This is the new because with OS-X 10.8.0-10.8.3 the active memory would go back to near the original allocation after a reboot. Now it won't, it will show the additional 400-500 MB's which doesn't seem to show where it's allocated.
And after having a lot of apps open and then closing them it will grow to 800 MB's to 1 GB's. Is there something OS-X is holding as active memory but is really inactive memory? I can't find any notes about what's happening or if this is just the new normal, that OS-X 10.8.4 simply uses additional memory.
I'm open to suggestions to find out what's happening.