Dropbox is NOT a backup
Have you made sure, the folders with those documents is not excluded via
System Preferences > Time Machine > Options?
What about starting from scratch with your Time Machine backups?
Time Machine FAQ
Anyway, I use
DropBox to backup and synch my important text documents.
For my systems I use a daily backup schedule via
CarbonCopyCloner.
Dropbox is NOT a backup service; it is a sync service. The Dropbox people are very clear about this. It syncs whatever is current on any computers that are linked to it. If you lose something on your computer, and Dropbox is syncing, you will lose it on dropbox. This means all computers, iphones, etc linked to Dropbox will lose it too. You can recover deleted documents for a limited time, but if you want to be able to recover them at any time later (say you don't discover it until a few months down the line) you have to pay extra.
Now, Dropbox only syncs files/folders that you have put in the Dropbox folder. This means you have to put everything into the Dropbox folder that you want to have sync. You won't be happy about this if you keep stuff you are actively working on on your desktop, like me. It won't sync via aliases. This is a way around this. There is a little program called MacDropAny that creates symbolic links to any folder on your computer, and Dropbox will sync via these links. This works fine, but remember that everything accessed this way will sync to every device you have linked to Dropbox. Personally, I don't want everything on my desktop or in Documents to be showing up on my iphone.
You also have to be very careful how you do it if you decommission a computer, or you can end up erasing everything on all computers linked to Dropbox. There are a lot of threads on their forum from people who lost a lot of documents because they didn't understand the correct process, which is not easy to find instructions for on their website - you have to do a search in the forums, it's not in their help/FAQs info.
You can also end up with duplicate Dropboxes if you unlink and relink. This can take up a lot of room on your hard drive. And if you use Parallels, DON'T link the parallels VM as a separate machine - I ended up with 4 copies of dropbox - what a mess! Instead, create Dropbox on your Mac OS and access it as a shared folder from Parallels.
Despite all of the above, I think Dropbox is an excellent service. Just don't think of it as backup. As my dad used to say, "Use the right tool for the job." I have had much bigger problems with iCloud, which provides a similar service.
I have not had any problems using Time Machine as a backup, except when I ran out of room. I have been told that you need twice as much room on a backup drive as you are using on your computer's drive. It's possible this is why it is not backing up everything. Larger capacity external drives are getting cheaper and cheaper, especially if you get slightly older models. I can't afford Time Capsule, so I use Time Machine as a manual rather than a constant backup. I don't use CCC or anything else, because as I understand it, Time Machine IS creating a disk image of the whole machine, not just backing up files. You can select folders in Time Machine Preferences if you want (you do want to exclude the backup drive itself here). I just click Backup Now. That's it. You can find and restore anything from an individual file up to the whole machine very easily. It's very simple to use and it works. Period. What I like about Apple products.
