I have a similar set-up to yours, and even when using the "Windowed" setting in SH4 (Options menu, Graphic Settings, to the direct right of the Resolution settings), it still minimizes the window. Now, big warning here: the game DOES NOT LIKE IT when you change Windows' focus to something else. The main reason for this is that the program was written to the Windows XP standard, and there is no provision for "virtual assets" in its address space. XP used exclusivity. If a game wanted the video stream, it was assigned a segment for the video stream. Audio the same way, etc. The game had an assigned address for each of the streams it uses. With Vista onwards, that address is "virtual" and might change when the focus comes back to the game, and those areas could well have been moved to a new location in the address space. SH4 does not know to "ask" the OS for the new addresses, and takes off from where it was with the old addresses, sometimes overwriting its own data in the process. This can cause all sorts of little nigglies in the game, like the 02 meter getting stuck, graphics glitches, such as a cloud of steam over the top of your boat, or any one of a number of other ailments, up to and including bad Save data and CTDs. It is recommended that you NOT change the "focus" from the game. What I now do is use a small tablet to hold my game tools, and it's actually a bit easier to deal with like that anyway, other than the screen "blanking" just as I go to copy the data over...
- an old laptop would probably work even better, if I had the desk space.
