The -u switch in rsync does not work between different file systems so it seems. It is supposed to ignore existing files in the destination directory, but it doesn't - well at least it doesn't between UFS and EXT3 in my doings.
Using the --size-only switch along side -u is a work around.
Example rsync for my reference:
rsync -airu --size-only /source/dir /dest/dir
-a archive mode
-i itemise change summary
-u ignore existing files