s3cmd sync is remote copying the wrong files to the wrong locations - bash

Question

I've got the following as part of a shell script to copy site files up to a S3 CDN:
for i in "${S3_ASSET_FOLDERS[#]}"; do
s3cmd sync -c /path/to/.s3cfg --recursive --acl-public --no-check-md5 --guess-mime-type --verbose --exclude-from=sync_ignore.txt /path/to/local/${i} s3://my.cdn/path/to/remote/${i}
done
Say S3_ASSET_FOLDERS is:
("one/" "two/")
and say both of those folders contain a file called... "script.js"
and say I've made a change to two/script.js - but not touched one/script.js
running the above command will firstly copy the file from /one/ to the correct location, although I've no idea why it thinks it needs to:
INFO: Sending file
'/path/to/local/one/script.js', please wait...
File
'/path/to/local/one/script.js'
stored as
's3://my.cdn/path/to/remote/one/script.js' (13551
bytes in 0.1 seconds, 168.22 kB/s) [1 of 0]
... and then a remote copy operation for the second folder:
remote copy: two/script.js -> script.js
What's it doing? Why?? Those files aren't even similar. Different modified times, different checksums. No relation.
And I end up with an s3 bucket with two incorrect files in. The file in /two/ that should have been updated, hasn't. And the file in /one/ that shouldn't have changed is now overwritten with the contents of /two/script.js
Clearly I'm doing something bizarrely stupid because I don't see anyone else having the same issue. But I've no idea what??

Answer 1

First of all, try to run it without --no-check-md5 option.
Second, I suggest you to pay attention to directory names, specifically trailing slashes.
s3cmd documentation says:
With directories there is one thing to watch out for – you can either upload the directory and its contents or just the contents. It all depends on how you specify the source.
To upload a directory and keep its name on the remote side specify the source without the trailing slash
On the other hand to upload just the contents, specify the directory it with a trailing slash