When setting a multiselect value, all existing options in db that match the value in a case insensitive way are also associated to the product.
Example: Given the following values in the eav_attribute_option_value table: hi, Hi, HI, an attempt to set the multiselect option hi to one product would set also the values Hi and HI to the product.
The problem is not directly related tu Magmi, but to the table definition in Magento, which does not specifies a case insensitive collate to the value column.
Possible solution: One approach to solve it is to force a binary string comparision. In the getOptionsFromValues() method (class Magmi_ProductImportEngine):
//... $sql.=" WHERE optvals.store_id=? AND BINARY optvals.value IN ($ovstr)"; //...