Using --link-dest works on small directory tree but not large one

[Robot Robot]

>
> You're asking du to report each directory separately, which is deceiving
> you.  Run "du -hsc /backup/websites" instead.
>

When I run that, it shows that there truly are two complete copies:

$ du -hsc /backup/websites
4.2G    /backup/websites
4.2G    total

I'm fairly certain du is intelligent enough to recognize hard links like
this and report the correct usage. (I'm using GNU du.) In any event, if what
you say were the case, why does du correctly report the disk usage on the
smaller directory tree?

Secondly, rsync *is* pulling down all the files again. When I manually rsync
the initial copy without using --link-dest, it takes 35 seconds to sync the
day's changes. When I use --link-dest though, it takes the full 3.5 hours
and more than 2G of network traffic gets received. Examining the verbose
output, rsync does not find any files "uptodate".

After playing with this some more today, I've noticed rsync will
occasionally but very rarely work correctly on the large tree. As far as I
can tell it's doing so completely randomly, and I can't find pattern or
salient factor that changes from one run to the other that makes it re-pull
everything. I can sometimes run it two or three times in a row, and it works
exactly like it should, and then on the subsequent attempt it will re-pull
the entire tree. Like I said, though, the majority of the time it is
re-pulling. Why is it doing this?
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