hmmmm .. one idea and a few more questions
1) Try lowering CHUNKS and/or BULKS. Refer http://faq.webyog.com/content/24/101/en/about-chunks-and-bulks.html. Note that the setting in ‘preferences’ has no effect for ‘scheduled backup’. The settings are in the wizard – please see image [attachment=2043:chunkbulk.jpg].
2) Can you view the table in SQLyog “Data” tab?
3) Is it a very big table?
If 1) does not help. I think you will have to contact your hosting support for help with this. There may be some permissions issue or some setting on this server allowing only small amounts of data to be processed per query.