I'm having this exact problem right now, i installed Sierra yesterday on my Macbook Pro and soon after it was finished i got back to work on my art program (i'm a Digital artist, so all my work is on a computer of sorts) but after a few strokes of my pen it always seems to think that i've clicked out of the program, and as Dimwhit said above, the program isn't hidden or anything, it's still on the screen, but i have to click back onto the program to continue working again...
I have to say though, that this is also happening on my iMac which had Sierra installed on it the day before, which also has the same program installed on it (my iMac is my main computer and my Macbook Pro is for when i'm travelling, which is a lot of the time so i need this to work like it was before i updated) So i'm facing this problem on both of my computers, i can't really escape it.
It's a huge pain to work with and seems to only be happening with my art program, Manga Studio 5 (basically a photoshop-like program), when Chrome is open as well as the art program and Skype it always seems to switch to Chrome as being the open and active application, then i have to click back to the program, it never seems to do this when i'm on Chrome for more than a few minutes, and it doesn't do it with anything else as far as i know...
I've unchecked the boxes in Mission Control like most of what searching on Google has told me to do but it doesn't seem to have done anything.....Is there anything at all i can do to stop this from happening? It's becoming very hard to keep focused on work when it keeps doing this.