I don't see the same behavior. Although I used small files, the below results plainly show it does not re-get:
C:\Users\Gregory\s3sync>s3sync.rb -r -v --progress ServEdgeTest: ./restore
Create node 100/ClearSigning.pfx
Create node 100/chain.cer
C:\Users\Gregory\s3sync>s3sync.rb -r -v --progress ServEdgeTest: ./restore
C:\Users\Gregory\s3sync>
Please try yours again but use -d so I get some idea what the generators and comparator are thinking.