No, not the same thing. When I first began seeing doctors for this ailment, Waldinger's papers had not yet been written and, as a result, I was often diagnosed with post-coital headaches upon explaining that orgasms brought about cognitive problems. This diagnosis didn't quite fit, though, as i've never had headaches. (I have a number of symptoms but headaches simply aren't one of them.) I imagine you don't either, and your doctor is simply trying to shoehorn you disease (which is admittedly fairly new and not an area of a great deal of scientific inquiry) into an established category.
As for the medicine you were prescribed, I'm highly doubtful it will work. (But you should at least try it, and if it does work, you should be sure to let us know!) But some migrane/headache treatments are quite effective for us, as they work to reduce inflammation (which many researchers believe causes migranes and which Dr. Waldinger believes causes POIS). In my case, for instance, the post-coital headache diagnosis was actually quite helpful because I was prescribed Non steroidal antiinflammatories, which have worked wonders for me. But this success was entirely accidental. Many drugs used to prevent post-coital headaches shouldn't work a lick.
Do you know why your doctor didn't prescribe indomethacin?