What do you mean by 360 servo? If it's a modified servo that runs continuously (like the 2 in the EZ-Kit) then it wont stop since it's position is never known, that's how they work.

to add to rich.

if you always calibrate the servos on the same ports(don't unplug them between calibrations) then just edit the script and take out the ports that the modified(360) servos are plugged into.

I recommend following the calibrate servo tutorial on the support page. Click support from the too menu. The Calibrate servo tutorial is a amongst the list. The tutorial video and written explanation will assist you there is no mention of calibrating modified (360 degree) servos. Only the standard servos should be calibrated before building your robot good luck!