I have downloaded the latest version (7.0.0.2038) of Toad for MySQL and when I try and compare 2 database schemes there all of the Procedures and Functions show as different, the tables and views work as expected, showing various difference in some of the tables that truly are different. When there is a difference in a table, the lines at variance are highlighted. With the procedures, even though it is flagged as different, none of the lines are mark. I have also noticed that the scroll lock between the two windows does not hold. The this case the databases are on two different machines, but both are Ubuntu with MySQL 5.5. NB: I have looked at all of the compare options under tools and can't see anything there that will help (possible white space issues?)
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