Nope, it will close out a leg. If that doesn't satisfy margin req. it will close the other leg. Did you try setting liq. last from the account page? Under the portfolio section you can use right click to set it. There are no guarantees that liq. last will follow your instructions. I'd assume that you are trying to set it on the long option, because the short option is where the bulk of the margin req. is.
On the portfolio page of TWS, I can set liquidate last on individual options, unless they're part of an option combo. Set Liquidate Last is greyed out for the synthetic short overall + both legs of it.
How do you disaggregate it so it shows the synthetic short as two unrelated option positions? that would probably fix my problem.