http://dl.dropbox.com/u/39311950/InflightAlign_JDAMsBroke.trk
(Edit: I haven't actually watched the track, so if it looks more like I just exploded on the runway, that's wrong...)
Here's a short track of Inflight Alignment and takeoff from Batumi, something close to how I'd scramble ... still need practice there. (Yes, there's a ton wrong with this startup, but if anything specifically other than the EGI alignment is causing the JDAMs to not arm, please point it out.) No warning lights, no master caution aside from the APU Generator, and the JDAMs list themselves all as ALN UNS.
There's nothing in the flight manual that says they require a 4 minute alignment. If that's the case, fine, but I want something that says that other than our observations.