Hi,
The buffer size is limited by the port itself. Consequently there really is no way to increase its size. Are you using VISA or the old serial VI's? One thing you may want to try is making your read time half the time of the write sequence. Also make sure that flow cotrol is working. With flow ctrl, you should never lose any information.
Hope this helps out.
Best Regards,
Aaron K.
Application Engineer
National Instruments