I'm guessing that if the scripts are taking that long you have some loops in there. One way to stop the scripts is to have the stop button set appdata that signals to the scripts that they should stop running. The loops in the scripts should check to see if this signal is telling it to stop or not before each iteration.
sample:
stopbutton callback
setappdata(0,'stopreq',1)
end
functiontostop callback
if ~getappdata(0,'stopreq')
code here
else
setappdata(0,'stopreq',0)
break
end
for this to work the functiontostop must be interruptable.
