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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: 2.5.11
PHP version: 5.4.16
MySQL version: 5.5.27
Host: (optional, but it helps us help you)
Akeeba Backup version: Akeeba Backup Core 3.7.7 (2013-05-11)

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 already tried several value combinations in Minumum/Maximum execution time, execution time bias and in number of rows per batch (Database backup engine) parameters. Unfortunately I didn't kept record of all these combinations. I just remember the last ones:
Min,Max,bias,rows
1,2,25,500
1,2,25,300

I tried also several time the configuration wizard without real success. I mean that some time the backup workds and then starts failing again.

Thanks in advance

My site has been upgraded to Akeeba BackUp 3.7.10, and still the problem exists. I am sending you the new log file.

i got again the same error. sending you the new log file

Dear Nicholas,

I tried your recommendation but unfortunately it made no difference. I also investigate more the problem and I still believe that is related with the akeeba backup engine in combination with server configuration. So let me give you some information about the server environment and the last symptom hopping that you might come back with some positive ideas if not with a solution:

1) The operational platform is Windows Srv 2008 R2 Std SP2
2) For activating the frontend backup is used the wget tool of GnuWin32 (GNU Wget 1.11.4)
3) The actual command looks as follows
D:\GnuWin32\bin\wget --max-redirect=10000 --append-οutput=d:\Backup\Backup_wget.log "http://www.mydomain.com/index.php?option=com_akeeba&view=backup&key=myfekey"
4) The backup script is implemented as vbs and is executed via windows task scheduler under the context of a separate user that is member of the local administrators group
5) In the backup script are executed two wget commands for two different sites. The first always succeeds when the second sometimes fails with the following symptoms:

The attached file is the backup log file and the output file of the corresponding wget is the following:
--2013-08-06 14:25:43-- http://www.mydomain.com/index.php?option=com_akeeba&view=backup&key=myfekey
Resolving www.mydomain.com... 192.168.0.26
Connecting to www.mydomain.com|192.168.0.26|:80... connected.
HTTP request sent, awaiting response... 303 See other
Location: http://www.mydomain.com/index.php?option=com_akeeba&view=backup&task=step&key=myfekey&profile=1 [following]
--2013-08-06 14:25:45-- http://www.mydomain.com/index.php?option=com_akeeba&view=backup&task=step&key=myfekey&profile=1
Reusing existing connection to www.mydomain.com:80.
HTTP request sent, awaiting response... 500 Internal Server Error
2013-08-06 14:26:17 ERROR 500: Internal Server Error.

As you can see there is no any serious delay between the last response and the error 500, just 32 secs.

Regards

Dear Nicolas,

Indeed the problem was the PHP max_execution_time limit. I changed to 60 secs and so far the backup procedure looks just fine. Hopping that it will continue like this I am closing this ticket.

Thank you very much for your valuable help in solving the issue.

Best regards