I am sorry, but I am not sure that I understand. Could you explain more in details? example? Screenshot?
With SQLyog 5.1x the .sql file is encoded using UTF8 on MySQL versions that support that. That is 4.1 and greater. A .sql file that is UTF8-encoded and has accented charracters cannot be read correctly with MySQL 4.0 and lower.
Is this the issue? What are the MySQL versions involved?
The backup 'powertool' of SQLyog ENTERPRISE has an option to deselect UTF8 encoding – also when exporting from MySQL 4.1 and higher.