Hmm, I can see if I get the same problem on my shaman. When I next log in that is
Hmm, that icon looks like its your mana spring totem, you sure that wasn't up either ?
Ah, just realised you mentioned it happens when you dual spec. May be all tied in with some cooldown issues we're having that may not necessarily be linked to nUI. I am guessing they made some changes regarding cooldowns when shifting specs. My shammy can't dual spec yet so can't test that side of it but I haven't noticed my guild leader who shifts specs daily reporting anything more than a cooldown message error before the more recent release came out. Since he downloaded the new one he hasn't reported anything but I'll ask him to watch for it.