Hmm, well often garbage collection is done at reboot, but that would mean that someplace in /home contains rapidly collecting garbage files. (Everything from java collections to temp files).
It could also be related to updates. Common on web servers, but anything that writes large amounts or large files can cause it.
Here's how it works;
If something is writing large files (or large numbers of files) and something else (or the program itself) is using those files, a filesystem will delete the files as requested -- thus showing up in df as gone -- however the program has not released the file until IT is finished with it(them).
This could be why you see it fixed when you reboot, system does clean-up at reboot.
Starting and stopping the program which is making use of said files would help, but then you are not sure what that might be. Merely deleting files which are in use does not alleviate the issue.
Putting a syslog rotator in place helps the situation, but first you have to find out what -- if anything -- is writing to the home dir, or some recursive dir contained therein.
The first thing I would do is examine every running userland proc, and find out form their configs where files -- if any -- get written. If any start out with /home OR if they write to someplace else which is sym-linked to someplace in the home dir space, you may have found your culprit.
That's my best guess at this point. Without doing any more intensive investigation anyway.
Cheers.
"It's always a long day, 86,400 won't fit into a short."