You went dual too, which was smart.
And yeah, I mean, I wouldn't have predicted a big dip like that either. Sealed subs do interact with a room differently tho, so I don't know what I would have expected. Messing around with placement might help a lot and having 2 gives you an even better chance. They may be cancelling each other out somehow too so playing with phase might help.
REW and a mic is really, really useful if you wanna get serious and dial it in. Really let's you see what's going on and a sweep only takes a couple of seconds. Audyssey is more cumbersome and I'm not really sure how accurate it is. A few of us have gotten some really good results with a MiniDSP 2x4 HD also, but with the Audyssey app out now you can achieve pretty much the same results.