A stupid bash script I wrote because I'm not clever enough to not have to write this.

sync.sh

#!/bin/bash
SRC=$1
DST=$2

if [[ -z ${SRC} ]]; then echo "No source dir"; exit 1; fi
if [[ -z ${DST} ]]; then echo "No destination dir"; exit 1; fi

for d in $(ls $SRC); do
    if [ -d "$SRC/$d" ]; then 
	      CMD="rsync -r $SRC/$d/ $DST/$SRC/$d"
	      echo $CMD
	      time `$CMD`
    fi
done

After an initial copy that looked like:
cp $SRC $DST

Sets up a copy of the first dir at the second location, this thing then syncs the sub directories omitting "hidden" directories.

I put the timing info into the command so I could figure out which dirs were going to be trouble.