mysqldiff tool drops indexes and adds duplicates and causes errors - mysql

Question

I'm using the mysqldiff tool (v1.5.3) from MySQL to synchronize the schema between two databases. The databases should have the same schema, but would like to produce a file that only has the ALTER TABLE differences between them so it can (after thorough testing) be run in production.
The problem is that the mysqldiff tool produces some weirdness. For example:
ALTER TABLE `database1`.`ACCOUNT_TRANSACTIONS`
DROP INDEX MATCHING_TRANSACTION_ID,
DROP INDEX PAYEE_ID,
ADD INDEX CHECK_NUMBER (ACCOUNT_ID),
ADD INDEX PAYEE_ID (PAYEE_ID),
ADD INDEX CHECK_NUMBER (PAYEE_ID,CHECK_NUMBER);
It seems to not only drop the indexes, but tries to recreate the new index through two statements that produce an error. The final schema should have CHECK_NUMBER (ACCOUNT_ID, PAYEE_ID, CHECK_NUMBER) as the index.
What might be causing this?
Final version:
CREATE TABLE `ACCOUNT_TRANSACTIONS` (
`TRANSACTION_ID` int(12) NOT NULL AUTO_INCREMENT,
`ACCOUNT_ID` int(1) DEFAULT NULL,
`REF_NUMBER` varchar(15) DEFAULT NULL,
`PAYEE_ID` int(6) DEFAULT NULL,
`ACCOUNT_CHART_ID` int(12) DEFAULT NULL,
`TRANSACTION_AMOUNT` decimal(10,2) DEFAULT NULL,
`TRANSACTION_DATE` date DEFAULT NULL,
`MEMO` varchar(100) DEFAULT NULL,
`ACCOUNT_BALANCE` decimal(10,2) DEFAULT NULL,
`DEBIT_OR_CREDIT` char(1) DEFAULT 'D',
`MATCHING_TRANSACTION_ID` int(11) DEFAULT '0',
`RECONCILED_DATE` date DEFAULT NULL,
`RECONCILED_EMPLOYEE_ID` int(12) DEFAULT NULL,
`TIME_UPDATED` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP,
`CHECK_NUMBER` bigint(20) unsigned DEFAULT NULL,
`STATEMENT_ID` int(12) DEFAULT NULL,
PRIMARY KEY (`TRANSACTION_ID`),
KEY `PAYEE_ID` (`PAYEE_ID`),
KEY `CHECK_NUMBER` (`CHECK_NUMBER`,`ACCOUNT_ID`,`PAYEE_ID`)
) ENGINE=InnoDB AUTO_INCREMENT=xxx DEFAULT CHARSET=latin1
Original version (needs to be altered to be final version)
CREATE TABLE `ACCOUNT_TRANSACTIONS` (
`TRANSACTION_ID` int(12) NOT NULL AUTO_INCREMENT,
`ACCOUNT_ID` int(1) DEFAULT NULL,
`REF_NUMBER` varchar(15) DEFAULT NULL,
`PAYEE_ID` int(6) DEFAULT NULL,
`ACCOUNT_CHART_ID` int(12) DEFAULT NULL,
`TRANSACTION_AMOUNT` decimal(10,2) DEFAULT NULL,
`TRANSACTION_DATE` date DEFAULT NULL,
`MEMO` varchar(100) DEFAULT NULL,
`ACCOUNT_BALANCE` decimal(10,2) DEFAULT NULL,
`DEBIT_OR_CREDIT` char(1) DEFAULT 'D',
`MATCHING_TRANSACTION_ID` int(11) DEFAULT '0',
`RECONCILED_DATE` date DEFAULT NULL,
`RECONCILED_EMPLOYEE_ID` int(12) DEFAULT NULL,
`TIME_UPDATED` timestamp NOT NULL DEFAULT CURRENT_TIMESTAMP ON UPDATE CURRENT_TIMESTAMP,
`CHECK_NUMBER` bigint(20) unsigned DEFAULT NULL,
`STATEMENT_ID` int(12) DEFAULT NULL,
PRIMARY KEY (`TRANSACTION_ID`),
KEY `PAYEE_ID` (`PAYEE_ID`),
KEY `MATCHING_TRANSACTION_ID` (`MATCHING_TRANSACTION_ID`)
) ENGINE=MyISAM AUTO_INCREMENT=xxx DEFAULT CHARSET=latin1