This sounds like an issue of "focus", i.e. in order for the keyboard commands to be directed to the keyboard, the window with the keyboard in it ( or is the application that is giving you the ability to play midi notes with your laptop keyboard) has to have the focus, or be the "selected" window. I am assuming that your keyboard is in ableton, so when you tweak parameters in oberheim SEM the focus goes to SEM (even if you are using your mouse only - focus is usually determined by mouse clicks, but the keyboard input goes with it).
It is even possible that focus can be directed to submenus or dialogs within an application, away from the main window, or a separate window that controls the keyboard to midi action.
I have this same issue in Reason, I haven't ever found a workaround. It is kind of deeply ingrained in the whole mouse-keyboard-multiple window paradigm, there is no way for an application to know when it could "steal" the focus. ( Imagine ableton having to decide that you were done editing in SEM and suddenly taking away your keyboard input while you were entering data.) I think it might even be almost impossible to write an application (in this case SEM) that would automatically release focus to the previous application. The only thing I could imagine is if there were NO alpha key use in a program that it could "defocus"...
I realize that I don't know if any Arturia synths recognize keyboard input to trigger notes....just checked Analog Lab and Modular V, seems they are only mouse trigger. Seems like Arturia could add this feature, and just disable it during dialog text or numeric entry. Sure would be nice for exactly the application you're talking about here.
I recommend the Korg Nano key mini USB controller, this thing fits in my laptop bag and actually sits on the front of my laptop in front of the keyboard (covering the touchpad but I also use a Microsoft Explorer wireless USB mouse that I also highly recommend). The mouse has a thumb button that opens up a magnifier window, this way I can run in high resolution and still read the fine print on the synth panels!
Cheers, Zip O'