time machine not completely backing up certain folders
Has anyone run into a problem with their Time Machine continually neglecting to backup one or two of their folders? I know some people have problems with TM not backing up items on their desktop, but my desktop data is fine. There are just two folders (as far as I know) that TM refuses to back up (unless there are new items, then it will backup only those items). One is my 'documents' folder. And another folder I created called 'OS media'.
About my setup:
I recently set up Time Machine with my Macbook Pro (running Mavericks). TM is backing up the internal SSD along with an external hard drive that is always attached via USB. The drive they are being backed up onto is a Western Digital My Book Live via wifi--which I know is not advised as it is not officially approved by Apple, but I'm hoping that's not the cause of this particular problem. Because otherwise the MBL has been working pretty well.
More details:
Both of the problem folders happen to be from the external hard drive (not internal SSD), and in the first tier of folders. But the other folders on that tier (about five other folders) are fully entact in TM, so I don't think it's an issue with the external HD. And the missing files are not a certain file type, they are all the sub-folders and files under the problem folders.
I went into the Western Digital (Time Machine) drive itself via Finder and verified that the files are indeed missing, so it wasn't a lag issue. And I have nothing excluded from backups in TM preferences.
I noticed that within those two problem folders, if any file was modified or created within that folder since my initial TM full backup (about two weeks ago), even if it was just a modified .ds_store file, TM would begin to include that file in the backup. This make me guess the problem was something that happened during the initial TM backup. The folders were somehow missed, and subsequent TM incremental backups aren't able to detect that it's missing. So unless anyone has any other suggestions, I'm just going to try to redo a full backup. I'm reluctant though, because it's going to take about two days to complete, and I really have no idea if it's even going to help.
And I don't know if this is related, but when I'm in Time Machine and I do a search for any of my files, I always get zero results.
Important sidenote:
While browsing my folders in Time Machine (Star Wars view), I found that clicking on an alias to a folder would open up that folder, but it didn't show the contents of the folder as they were in that particular backup version; instead, it showed the contents of that folder as they appeared in my computer currently. In other words, it appeared that I was looking at an old backup version of the folder, but it was actually the present time folder. This could easily mislead someone into thinking that their current data is backed up, when it is not.
MacBook Pro (Retina, Mid 2012), OS X Mavericks (10.9.2)