This seems to be the same bug: https://code.google.com/p/heidisql/issues/detail?id=3542
When adding a BIT field longer than 8 bits (16 bits in my case), only the last 8 bits (ranging from dec. 1 to 256) are shown in the table data tab and in query results.
When viewed in PHPMyAdmin it shows the correct value (including the first 8 bits).
In short: when entering 0000011000111000 as value in a BIT(16) field, the full 0000011000111000 is stored, but when viewed as data or if queried, only 00111000 is returned.