In the image above I have OTItemEditor 0.3.9 in Wine, and Google in Firefox. I was clicking the Google's search box, but Wine was always on top, it wouldn't lose focus. If I try to type anything it would still be inputted in Wine.
If I try to minimize Wine, it would minimize to the corner but it would still be focused:
The only way that I can focus on the window I want is using Alt+Tab, otherwise it is always focused in Wine. I don't know why, but sometimes it changes focus on click, but it's rare.
This is often an issue that is Desktop Environment/Window Manager specific. What DE are you using? Don't forget that Wine just sends the draw commands for application windows via requests to the X Server stack. This can result in windows being drawn in the wrong order (from that expected under native MS Windows) - focus issues are typically more up to the Linux DE.
Just tested out the application on Arch with Wine 1.7.12 & KDE (obviously without database files). I'm not seeing any focus issues...
