Simple tests worked fine, but after uploading the RepRap host software at 115200 Baud, had problems connecting and even uploading new sketches. I had to press reset and upload almost straightaway, otherwise the upload failed.
A bit of research suggested an updated Atmega 8u2 firmware (the usb chip). (also the new boards appear as /dev/ttyASM0 instead of /dev/ttyUSB0 - update to the latest RXTX libraries.
Borrowed from a forum post by stimmer on this thread
Also, a good page on the arduino site
Note, that to put reset the Mega 8u2 chip, the reset pins are a bit different: I found instructions for resetting the mega chip.
Might help if you're getting unreliable high-speed connections to the arduino and you've got a recent board (/dev/ttyACM0)