The script in the GUI is only saved when you actually save it, and the path you mention is the default location.
When using the command-line you use the /ScriptFile switch to specify the path/filename to save.
You can also use the /sync switch to synchronise the changes directly; but it should remove any temporary files afterwards.
See here for details on switches: http://www.red-gate.com/supportcenter/Content/SQL_Data_Compare/help/9.0/SDC_CL_Switches
If you want to specify a bigger drive for temp files, you can create an environment variable called RGTEMP and set that to the path you wish to use.