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Mandatory information about my setup:

Have I read the related troubleshooter articles above before posting (which pages?)? Yes
Have I searched the tickets before posting? Yes
Have I read the documentation before posting (which pages?)? Yes
Joomla! version: 2.5.4
PHP version: 5.2.17
MySQL version: 5.1.62-rel13.3-log
Host: Site5
Akeeba Backup version: 3.4.3

EXTREMELY IMPORTANT: Please attach a ZIP file containing your Akeeba Backup log file in order for us to help you with any backup or restoration issue. If the file is over 2Mb, please upload it on your server and post a link to it.

Description of my issue:
I upgraded to Akkeba Core 3.5.0 and experienced a 500 (Internal Server Error). I did what was suggested in tix #12320 but it didn't fix the issue. I restored an old backup running 3.4.3 (see error log attached) but am now getting the same 500 Internal Server Error. Before upgrading Akeeba worked fine. This is a subdomain so I don't know if that has anything to do with the issue. The other site I have the same issue with is also a subdomain. Any ideas? Thanks.

Follow Up:

This is a follow up to the second site referenced above "The other site I have the same issue with is also a subdomain".

Joomla! version: 2.5.4
PHP version: 5.2.17
MySQL version: 5.1.62-rel13.3-log
Host: Site5
Akeeba Backup version: 3.5.0

I am running Akeeba 3.5.0 on this site and was getting the same 500 Internal Server Error. I checked the option to use iframes instead of Ajax and was able to make a backup. Next I replaced a few images on the server and tried to do another backup and received the follow error "Invalid AJAX data". I have attached the error log for this site (subdomain) as well.

Akeeba Backup should run fine on subdomains.

You went through and renamed the directories as noticed in the ticket you referenced? You didn't just overwrite the install without that, correct? You didn't uninstall or downgrade?

What what I can see in the backup log, it doesn't look like it actually completed. Because it is a 500 error that is thrown, it doesn't show up in the backup log in this case. When the error occurs, check the error log (not the access log or backup log) and see what error is being thrown in there. A 500 error should report in the php error log.

I first upgraded via Joomla backed extension manager (to 3.5.0) and did a backup that gave me the 500 Internal Server Error. I then performed the steps in tix #12320 and reinstalled 3.5.0. When I ran it again I get the same error. That is when I restored the original BU with 3.4.3 and I still get the same error.

Error Log:[Thu May 17 17:31:55 2012] [error] [client **.**.**.193] File does not exist: /home/my-site/public_html/sub-domain/500.shtml, referer: http://sub-domain/administrator/index.php?option=com_akeeba&view=backup

Update:

Site5 was kind enough to help with the following settings that seemed to do the trick:

Archiver Engine set the "Part size for split archives" to 127Mb or less.
Minimum execution time: 10 seconds
Maximum execution time: 7 seconds
Execution time bias: 50%

That would explain why the restored version didn't work after running the config wizard. They claim nothing was changed on their end in the last week. I don't know but I am glad it is working. Hopefully these settings help someone else.

Cheers!