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I really don't understand what you are saying.

You said you "looked at the docs and the file is not there". Which documentation did you look at? I wrote all of it and I'm pretty sure I don't mention anything about those files.

Then you say "I noticed the file was intentionally removed for the latest version". Um... no? I am quite sure that media/com_akeeba does exist and it's absolutely necessary for the correct operation of Akeeba Backup. This certainty springs from the fact that I am the developer of the component and know exactly what's in that directory. The only thing that did change several versions ago is that there is also another directory, media/akeeba_strapper, with the same permissions requirements for itself and its contents.

Then you say that "all of the permissions are set correct". Now you totally lost me. I mean, the way I read your post you're saying that the entire media/com_akeeba directory isn't there, then you say that its permissions are correct. How is this possible if it's not there.

Sorry, I don't know how to help you except repeating what the error message says: please check that media/com_akeeba exists and check the permission of this directory and all of its contents. If unsure, please install the component again, but without uninstalling before the reinstallation (otherwise you'd lose all your settings).

OK, now I understand what you're saying. This file is now in media/akeeba_strapper and the same permissions requirements apply.

The only thing that definitely doesn't get in the way is JCE. I use JCE on all of my sites. Could it be a plugin? There's a 99% chance of that happening. I'd start with system plugins. Can a reinstall help? There's a 1% chance that it might help. I'd only try it if all else fails, that's why I didn't tell you to do that yet.

So, my advice is to first look for any system plugins which may be causing a problem on your site and if that doesn't help then try to reinstall Akeeba Backup.

The only thing that definitely doesn't get in the way is JCE. I use JCE on all of my sites. Could it be a plugin? There's a 99% chance of that happening. I'd start with system plugins. Can a reinstall help? There's a 1% chance that it might help. I'd only try it if all else fails, that's why I didn't tell you to do that yet.

So, my advice is to first look for any system plugins which may be causing a problem on your site and if that doesn't help then try to reinstall Akeeba Backup.

Wait, what? I thought that you'de get this error message as soon as you tried visiting the Akeeba Backup Control Panel page. The fact that this happens during backup is news to me. In this case we're talking about a different issue. Does your computer goes to sleep while backing up? That would explain both the strange error message and the backup failure.

I would first try setting a higher part size for split archives (10-20Mb) and unsetting the upload immediately option from the S3 post-processing settings.

If that still doesn't work I'd try a files-only backup so that the database doesn't get in the way.