Changing storage engine to InnoDb from MyIsam is dropping records from table

Currently our Database all tables are using MyIsam as a storage engine. We tried changing storage engine of our mysql tables from MyISAM to InnoDB from PHPMyAdmin operations tab. However during the change table records are dropped. So what can be the possible factor causing this problem. This is what we tried: We converted test_user table which was having storage engine MyIsam and was having total records 11k. When we converted it into InnoDB the records droped to 9k. This happened for many tables. Not sure what we are doing wrong.