Depends on the exact circumstances, but try this. Go to "Settings > Plugins and Extras > Debugging > Advanced", enable the option "Keep Foreground Lock Timeout", and restart Dexpot.

Is there a way to prevent apps from stealing focus on background desktops on Windows 7?

It's very annoying when a program launching on f ex Desktop 2 grabs focus while i'm doing things on Desktop 1. I have some automated scripts that launch new applications every now and then and every time the app launches, it steals focus, even if it's not on the current desktop. Lose a lot of typed text and sometimes the key presses do actions in the background app which is very unwelcome.