* use a real boolean column in their schema (I mean, the data you're representing IS a boolean value in this case, right?); or * use setObject(column, value, Types.SMALLINT) instead of the implied setBoolean() call when setting the column (this may be tricky to do since you have a layer between you and the driver, but that's not really the driver's fault..); or * add a suitable implicit cast on the backend side from boolean -> smallint (not sure if this works, haven't looked at the details)
I would actually suggest running your problem past the hibernate community. It seems unlikely that you're the first team to encounter this problem. How do you have the property mapped in the hibernate mapping? Is it possible that explicitly setting the hibernate type of the property in the mapping will solve your problem?