I have coupled my Gmail account with Mail.app on Mountain Lion. Sometimes I search for old messages, only to find out that the message is there, but without any content. Checking the raw source also only shows the header without content. It looks like this:
Sometimes the message will load after a minute or two, but then Mail hangs (this does not show in Activity Monitor though). I then need to force quit the application.
I have no plugins installed, I tried the rebuilding/reindixing steps shown here, but it didn't help.
The message shows fine in the Gmail web interface.
I found different messages from different senders with this behaviour, without showing an obvious pattern. If the blank messages contained an attachment I could Quicklook / open it.