Ah, yeah. You'll want to download and run the real time kernel (synaptic search), and then put the following into terminal:
Then reboot the computer. You'll also need to install the real time kernel restricted modules package (again, synaptic search) if you use the nVidia or ATI graphics card drivers. Once you have that done, start up qjackctl again, but before hitting that green arrow, go into settings and enable real time mode. If your DSP can handle it, crank the sampe rate, too. That will lower latency.
:-$ sudo su -c 'echo @audio - rtprio 99 >> /etc/security/limits.conf'
:-$ sudo su -c 'echo @audio - memlock 250000 >> /etc/security/limits.conf'
:-$ sudo su -c 'echo @audio - nice -10 >> /etc/security/limits.conf'
I believe that should solve your problems.