I think this might just be an artifact of how the chunks get uploaded being confusing in the log. The chunks get buffered into memory first so as far as the rclone progress indicator is concerned they've been sent at that moment. This works better on some backends where the chunks get read byte by byte, but in the s3 backend it reads the whole chunk first to calculate its SHA256 for uploading.
The important question is, is it filling your upload pipe?
It seemed to take 9 minutes to transfer 3.1 GiB which is 5.9 MiB/s or 49 Mbit/s. Is that about the speed you are expecting?
This is odd though, it seems to say that the transfer speed was 0? Was that the last speed log rclone printed?