A few months ago we had a mandate to connect a BS240 to our LIS Silabmed(www.silabmed.com), it was not easy at all.
However integration with the Mindray BC20s and the Mindray CL-1200i and our LIS Silabmed was very quick and easy.
You are right we had problems assigning the samples to position, we had to rewrite this part of our library to overcome this problem.
Did you contact Mindray?
Try to get support from them, they may a new version of their firmware that solved this problem.
If you get lucky let us know.