There has not been any changes to the http module. The S3 backend uses the standard Mono http(s) connections. I am guessing that there is a problem with a timeout somewhere that does not kick in.
It should work such that the timeout happens, causing the upload to fail, and then Duplicati simply re-tries the upload and all is good.
Unfortunately, due to the way web connections are implementend in .Net (and the AWS library), we cannot replace the connection instance, so we need to figure out how to fix this through the AWS library.