1) Create a synthesis run, but instead of launching it select the "Generate scipts only" option.
2) Browse to theProject_Name.runs\synthesis_run_name folder and find the .prj file.
3) Edit the .prj file such that it lists the HDL files in the order that you want them to be compiled.
4) Open a 12.1 command prompt. On Windows go to Start -> Programs -> Xilinx ISE Design Suite 12.1 -> Accessories -> ISE Design Suite Command Prompt or on Linux open a terminal and then source the appropriate settings32/64.sh/csh file to setup the environment.
5) Browse to theProject_Name.runs\synthesis_run_name directory and on Windows launch the runme.bat script or on Linux launch runme.sh script.
This will launch the synthesis run as if you had launched it in the PlanAhead GUI, but it will maintain the changes that you have made to the .prj file.