When using make sync with an already built site, if wil take hard-copied directories (like data/ in the makefile for instance) and copy the entire dir into a subdir. For instance:
$ ls data/
file.txt index.html
becomes (after sync with contents already in build/):
$ ls data/
data file.txt index.html
I would assume that this is either an issue for rsync or make, but as a hack fix, you can just depend the clean make rule before all on the sync rule.
Issue seems to stem from make, not rsync.