Custom Menu Widgets won't stay in widget areas?

Hi, I've got a multisite setup. We're going to take one site we've already built and duplicate it twice, then modify each of the duplicates for various other online publications that are similar, but a little different. We used the New Blog Template plugin to duplicate the original (we've also tried BackupBuddy). When we do this, then add a Custom Menu widget to one of the new duplicate sites, it doesn't "stick." It appears there in the widget area, and such. But if you navigate away and back or just reload Appearance>Widgets, the custom menu is gone. We haven't tested all widgets, but others seem to "stick." Any ideas what the heck is going on? The original source site doesn't have this problem.