Support

Try setting the directory to joomla, without a leading or trailing slash.

No, I believe you misread the documentation. The documentation says much, much more besides the 49.99Mb part size. Actually, our troubleshooter reads:
""Finally, some hosts do not play very well with Amazon S3's multi-part upload feature which allows us to upload a very big archive file in 5Mb chunks. In this case you will have to follow Plan B which is to have Akeeba Backup split the archive file in small chunks, one file per chunk, and then upload each of those chunks in one go. This is a two-legged solution.

For the first leg of the solution, please go to Akeeba Backup's Configuration page and find the Data Processing Engine drop down. Click the Configure button next to it. A new pane opens below. Check the Disable multipart uploads option and make sure that the Process each part immediately option is not checked.

Now, for the second leg, we have to do some trial and error. Still in Akeeba Backup's Configuration page, find the Archiver Engine drop-down and click on the Configure button next to it. A new pane opens below. Find the Part size for split archives option and select the 49.99 option. Try a new backup. If it crashes while uploading files to Amazon S3, go back to this option and try smaller values, i.e. 20, 10, 5, 2 or even 1, trying a new backup after setting each one of those values.""

I am not sure why you skipped the first leg only followed through half of the second leg of those instructions. There's a reason I have presented this as a two-legged process. If you do half of half of it it's certainly not going to work :) If you do follow all three paragraphs you'll see that the upload to Amazon S3 will work. That means, I would recommend doing exactly as the troubleshooter reads, in the order presented:
1. Check the "Disable multipart uploads" option
2. Try gradually decreasing the part size
Usually we have good results with a part size around 10-20Mb.