Time Machine is skipping files and folders. How to fix?

Running OS X 10.10.2 on a Early 2009 Mac Pro. System installed on a 256 GB solid state drive. 10 GB of memory.

I'm having a problem with Time Machine where it's not backing up some of my files and folders. There doesn't seem to be much rhyme or reason to it, but it includes very, very important things like the parent directory for projects I'm working on, arbitrary hash directories in some git repositories, an assortment of emails, Messages attachments, random preferences files, and somehow the entire contents of my Pictures folder. And probably more -- I haven't checked everything.

I've recently forced Time Machine to do a full traversal when it made a recent backup (and confirmed that it was a full traversal by looking at backupd's output in Console.app), but these files are still missing.

I also tried going into one of the directories that wasn't being backed up and running:

find . -exec touch {} \;

to make every file appear to be recently modified, and then told Time Machine to make a new backup, but it still skipped them.

Does anyone have any suggestions for what I can do to fix Time Machine? I just want it to do a full backup, not skipping anything.

As a last ditch effort I could blow away my Time Machine drive and start from scratch, but I really, really don't want to do that because it contains several months worth of backups, and I occasionally do need to go back and get older versions of files.

Edit:

I haven't found a solution to this particular issue, but I have decided to discontinue using Time Machine for backups as I can no longer rely on it. I've decided to give ChronoSync a try since it seems pretty comparable.