I've seen that condition when the PC was running real slow (too many processes running in the background) thus causing interference with the MagicJack.exe process. Usually, after a PC reboot, the stutter is gone.
The actual dial tone is generated by the MJ dongle. Have you tried a different USB port? You might want to check running processes to see if there is a load on the CPU. Take a look into the plugs on the MJ and make sure they are clean. I've seen lint and dirt packed into USB connectors and RJ45/RJ11 connectors.
Have you tried a different phone? Is the phone you are using powered by batteries? The dial is going from the MJ directly to your phone if it is like other land line emulators, not thru the computer. Is it plugged into a hub or directly into the MB. Just wondering if a low power situation could cause it.