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I can't understand what you mean.

What does "i no longer have two recent S3 backups" means? Are the deleted from the server, deleted from S3 or you no longer see the backup records in the Administer Backup Files page?

I think that the problem is a stuck view filter. Just try logging out of your site and then log back in. Do you see the files now?

If you don't, I need you to ZIP and attach your backup log files. Without a log file, your guess is as good as mine.

Log file didn't make it. Please put the txt file in a zip file before attaching. If bigger than 2Mb, upload to a file service like DropBox, paste a link here. Thanks!

Your backup is stuck in a loop while trying to "update statistics", i.e. write information to the database table where all backups are registered. This means exactly one thing and one thing only: failed update. First, try to install Akeeba Backup 3.3.11's ZIP package on top of your existing installation and retry backing up.

If this doesn't work, follow this procedure:
- Keep a copy of your jos_ak_profiles table (and ONLY that table), using phpMyAdmin
- Keep a local copy of all of the backup archives you want to keep (they'll be deleted from the server)
- Uninstall Akeeba Backup
- Install Akeeba Backup Professional 3.3.11
- Restore the jos_ak_profiles table using phpMyAdmin

Perfect! I'm glad it's working now :)

The one-click upgrade doesn't suffer from the 2Mb limitation because you don't upload anything to your server :) In fact, the one click update is a four step process:
- The ZIP package is downloaded from our server to your server. This doesn't involve a download
- It is extracted
- The Joomla! extensions installer is called and told to install the extracted files
- The extracted files and archive are removed
This works irrespective of the 2Mb upload limitation and since each step is done in a separate pageload you are less likely to hit the timeout limit.

Moreover, the next version of Akeeba Backup will feature a much smaller package. I am removing all translations from the package, which means that we'll be saving about 1Mb from the package size. I am working on that right now!

That's why I'll be removing the translation files. OK, this didn't sound too insightful right? Let's take one step back and see what it means to install an extension.

First, Joomla! runs the SQL installation script. This is a very fast process, in the order of a few dozen milliseconds. Then, it starts recursively copying all files listed in the package to their final destinations. This is a O(N) process, meaning that the time it requires is directly proportional to the number and size of files. As a matter of fact, the main factor is the number of files. If you use Joomla!'s FTP mode in the Global Configuration, Joomla! has to initiate an FTP upload for each and every file. This can sum up to several dozens of seconds, leading to a timeout. The same holds true for the previous step of the installation, unpacking, as Joomla! has to upload each extracted file.

After analysing my extension packages, I saw that half of the files are translation files. However, not everyone needs all translation files, right? So, I'm going to remove the extra languages (two dozens of them!), reducing both the number and total size of files to copied. Therefore, the installation will need about half the time to complete, which is exactly what is required to fix your timeut issues.

Of course, the best workaround is using a very performant host, but not everybody can afford it (even if it's as low as 8$ per month) ;)