I suspect this problem is not with Gmail or changes Gmail has made recently:
I have 2 loaded iMacs, 2 Mac Airs,and a Macbook Pro with Retina, and 2 iPads, and an iPhone.
I have confirmed on all my iPad and iPhone devices that all my Gmail content is visible, and installing Thunderbird on the iMacs and MacBooks accesses Gmail and the sub-directories.
However, MAIL on the iMacs and MacBooks fails to access the Gmail sub-directory contents dated pre-OSX installation. I have kept everything updated.
PERHAPS NEW INFO TO THIS THREAD: Also, current Time Machine backups fail to show Gmail IMAP sub-directory contents dated pre-OSX installation as well, so this problem appears to be OSX UNIVERSAL not just affecting MAIL. (on one iMac, Mavericks trashed my Time Machine drive (Pegasus - but the company responded quickly with a fix but I lost all the backups). My other iMac (I have one at home, another at work) has a pre-OSX Time Machine backup still that Mavericks has not yet trashed (although it has tried in various ways). The pre-OSX backups show all my Gmail messages in all directories... but post-OSX install the directories show as empty.
Performing a 'Get Account Info' via MAIL 'sometimes' shows a correct Gmail sub-diertory message count, 'sometimes' does not, and 'sometimes fails to report the even the sub-directory name or stats. BUT, doing Show Messages, even whent the message count shows correct, displays an empty directory, or only those messages post-OSX install.
As someone posted earlier, go to 'MAIL' and select 'Provide Feedback' and bombard Apple Support with a bug report.
PS. Thunderbird will not install an iCloud account in IMAP for me, even a manual config from settings in MAIL don't work, and Thunderbird won't 'Import Settings' or 'accounts' or 'folders' or 'Local mail' from MAIL under Mavericks either it seems... reports Info Not Found.
PSS. installing an iCloud account did nothing useful to these problems, and in fact I had to go online into iCloud via the web to create a subdirectory before MAIL or even the iPads etc would see more than the iCloud Inbox.
PSSS. to get MAIL to refresh the Gmail Inbox, I have to shutdown MAIL and re-open it (and sometimes, MAIL takes a long time to shutdown as well).