Serial Port under Linux unuseable slow

Hello

I've recently written some kind of motor-control interface at work which communicates with a microprocessor from ST and sends/receives commands and data. At work I use R2013b on a Windows7 machine, together with an usb-serial adapter from FTDI. In combination with a serial callback which reads data-packages in known byte-sizes I could achieve 0.5MBaud which I would consider somewhat useable for a continuous data stream for a fast control application. On this point I was actually looking forward to run my application at home... on a Unix machine, with kernel-built-in ftdi drivers.

So far so good. Now back at home I'm on Linux on R2014b, sitting on the same code with exactly the same physical premises and the speed (or more precisely the slowness) is killing me. From my observation I'd say its not even the baudrate which can't be handled, its the sheer amount of data. Matlab is simply to slow to handle the callbacks...

How can that be? The computer I've at home has about the same amount of processing power and ram... Can this have something to do with the change to R2014b...? Or is it something driver related?

How can I speed up the communication?

tia