Here is what I did to get serial port communication work in Matlab R2014a on Arch Linux 64 bit:
1a) follow the steps described here: http://www.matlabarduino.org/serial-communication.html:
sudo chmod 777 /dev/ttyACM0
Alternatively, add your user to the group uucp: > sudo gpasswd --add username uucp
sudo nano $MATLABROOT/bin/$ARCH/java.opts --> add: -Dgnu.io.rxtx.SerialPorts=/dev/ttyS0:/dev/ttyUSB0:/dev/ttyACM0
1b) check that the connection works in gtkterm (select port ttyACM0)
2) additionally (critical only for Matlab):
sudo chmod 777 /run/lock
/run/lock was symlinked from /var/lock on my distro, so you might have to do this with the latter dir (was 755); alternatively, you can manage access rights to /run/lock/ by ACL.
How I got to this solution:
sudo strace -p 4668 -f -s100 2>&1 | grep -C3 --color -i -e /dev -e serialports -e uucp
-p: process ID == second column from > sudo ps -aux | grep -i matlab
Then, in Matlab type >> sps=instrhwinfo('serial') (which in my case always returned a structure of empty cell-arrays) and monitor the output of strace.
Hope that helps!
cheers :)