Search and destroy for offending programs
For debugging this type of problem, I would first check other programs running in the background. Some applications like real time virus detection, anticheat software, or "updater" applications may be trying to come to the front. You should be able to go into task manager (accessible when you press CTRL+ALT+DELETE) and kill most other applications. That's sort of brute force, but if you find the process that's causing you trouble by process of elimination, there may be a more graceful way of shutting it off from the application itself in the future.
It may be that Windows Defender is still your problem, even though you "disabled" it. One person here suggests updating to the latest version. Others have seen this problem with IM clients, and of course there is always Spyware. Here's a video with a walkthrough on killing potentially offending background tasks, though you may have to hunt a little hard than he did to find the process which is causing you trouble.
If you suspect Spyware, I recommend MalwareBytes and Microsoft Security Essentials.
Download latest graphics drivers
This behavior falls into the category of "graphics isssue". For any such issue, it's always a good idea to download latest drivers.
Try an autohotkey or similar script
You can use functions of windows to force your Bioshock window to always on top. A script will make it easier for you to do so, via hotkeys. You can download one such script here.