Something I recently ran across confused the heck out of me until I looked into it and figured out what was going on. I'm hoping that this message will help others resolve similar confusion.
I've been using LyX since at least the 1.6 days, and in all that time, Ctrl-Enter in math mode changed the equation I was editing into an "eqnarray" with a 2x3 shape. Recently, Ctrl-Enter started giving me a 2x2 "align" instead. The difference turns out to be whether or not the "amsmath" package is enabled explicitly or automatically in the Math Options section of the Document Settings. If it's set to trigger automatically, then it seems that regardless of whether or not it gets enabled, the "eqnarray" is used. Since I never needed to explicitly enable amsmath until I started working with parent/child documents, I never noticed this behavior until now. The behavior makes sense to me after I thought about it for a minute, but it was surprising nonetheless. I've seen this behavior in versions 2.0.3, 2.0.6, and 2.1.0 in (debian) Linux; and 2.0.3 and 2.1.0 in Mac OS X (where the keystroke is Command-Enter.) Wil Langford -- An apple every 20 minutes keeps 72 doctors away.