When you purchase apps (even free) on the device, iTunes always backs this up - and when it Syncs, before it does anything it backs up - and it notices that you have purchased an app/apps - so it wishes to make a backup of these apps. Click transfer and it'll all work fine - happens to me when I buy songs off of the store as well as apps
You can change the shortcut for "Close Conversation" to something else, that should avoid the conflict. To do this, open Keyboard Preferences, and then go to the "Keyboard Shortcuts" tab. Click Application Shortcuts, then the + button to add a new one. You should get a popup like this one (I'm still on Lion, but I don't believe they changed much):
Change the application to Messages, enter the proper menu title (if it uses an ellipsis, you may have to enter that exact character — not just three periods — by hitting optionshift;), then enter in a shortcut you're unlikely to use.
It's also possible to disable a keyboard shortcut from the command line, rather than just setting it to some obscure command. However I haven't tested this on Mountain Lion or Messages app, so no guarantees.
If you're comfortable with the command line, the proper command would likely be defaults write com.apple.Messages NSUserKeyEquivalents -dict-add "Close Conversation…" nil
. However I don't have access to Mountain Lion, so the com.apple.Messages part is just a guess. You may want to test first by trying defaults read com.apple.Messages
and see if it pops up with an error. It should spit out a long list of plist-formatted preferences, if it doesn't the app identifier (com.apple.Messages
) is probably wrong, so you'll need to do some digging to find out what it is.
Again let me stress that I haven't tested this second option on Mountain Lion or Messages at all, it's just based on how things work in previous versions of OS X.
Best Answer
The pref doesn't say "Save history when you quit or logout" it says "Save history when conversations are closed" - i.e., when you hit the X to get rid of them - either permanently, or temporarily, depending on that pref.
If you want to delete the archive itself, you'd have to do that manually.
Files live in
~/Library/Containers/com.apple.iChat/Data/Library/Messages