I've been involved in creating build scritps for Ax2012 over the last few months and have encountered (and conquered) a number of ... well, let's cal them 'obstacles'.
One of them is the 'the model store had been modified' dialog that pops up the first time you start an Ax client after the model store was modified. It actually gives you some options (start checklists, compile and sync or just skip the whole affair).
But sometimes this happens: you don't manage to select any option. I mean: you can click an option, but it does not get selected. In fact: the (modal) dialog (including the OK/cancel/close buttons) does not react at all.
My workaround is to start the Ax client directly in a developer workspace (ax32.exe -development), where you get the same 'modelstore modified' dialog, but it does react when you click it.
Another option is to undo the installmode setting on the modelstore (axutil.exe set /noinstallmode) which prevents the modelstore modified dialog from popping up, and fire the compilation, CIL generation an synchronisation (or any option you whould have chosen) manually.
Don't know why this happens, I just hope I save someone some valuable time with this workaround.