Long time back, i have used a FFAP column for analysis of fatty acids in Saw palmetto extract. It worked perfectly fine and i was using stearic acid as an internal standard. I did not develop the method and so i don't really know why an internal std method was setup.. May be you should try using some other fatty acid as an internal standard? offcourse, thats assuming that all you need is the assay of stearic acid in your samples. Also, i used the split mode to do it (with an Agilent 6890). I am assuming that you are in desperate need to improve your quantitation limit as you seem to prefer splitless. If you have enough analyte in your sample, then i guess split method should be the way to go.
When you say you cannot set up the calibration curve, what exactly do you mean? bad correlation? what is the R value for your curve?
Good luck!
Suresh.