Does your dataset consist of InnoDB tables with large BLOB data such that the data is stored in external BLOB pages? Was the dataset created in MySQL version 5.1 and below and without using the InnoDB plugin, or with InnoDB plugin but with MySQL version earlier than 5.1.55? If the answer to both the questions are "YES" then it could very well be that you have a hidden corruption lying around in your dataset.
Having reviewed different table structures designed by different people, I have come to the conclusion that binary and non-binary string data types are used without consideration of the consequences of choosing either one. The confusion stems from the fact that both non-binary and binary string data appear to store characters because they can be saved as quoted string.