ActiveX interacting with dialogue boxes

Greetings, everyone!

I routinely use activex to play around with excel files via matlab, but recently I've come across a bit of a hickup. I open a file with activex, but the file in question has links to other excel workbooks, and therefore a dialogue box pops up asking whether I want to update the values or not. The catch is that this dialogue box often appears "behind" matlab, so I don't really see it unless I know its there. The second catch is that I want to compile this script into a stand-alone, and I really would like to avoid explaining to various end users "yeah see, you have to sort of wait for this ping noise, and then alt-tab until you find the dialogue box, and then click dont update".

Does anyone have experience or advice on how to interact with popup menus via activex?