Thank you very much for your reply.
The bottleneck here is not really the hardware (the relatively slow speed of rs232) but poor programming (on both Matlab and Windows side). With 115200 baud (which is the standard maximum speed of the com port), it is possible to achieve 11520 bytes/s "real-time" transmission using 8 data + 1 start + 1 stop bit (without even using the FIFOs). In fact, if I remember correctly, I was achieving this data rate with an i486 running at 33 MHz. Now, I can not achieve a rate faster than 100 bytes/s with a 3.2 GHz dual core i586.
The potential "real-time" transmission rate of the serial port is not really that bad at all (11520 bytes/s). However, thanks to the excellent utilization of hardware resources in Matlab and Windows, we can not even achieve 1/10 of that available capacity. Unfortunately, buffering the data is not a solution as the communication is supposed to be "real-time".