https://bugs.winehq.org/show_bug.cgi?id=44032
--- Comment #10 from Adam Bolte abolte@systemsaviour.com --- Thanks Steve - that's exactly what it was. I tested various combinations of the options listed under the winecfg Graphics tab, and what I discovered was that in addition to the patched version of Wine, "Automatically capture the mouse in full-screen windows" needs to be disabled, and "Emulate a virtual desktop" needs to be enabled. Setting "Desktop size" to the same resolution as my monitor worked best - 2560x1440 in my case. I tried 1920x1080 initially, but then the keyboard wouldn't work and the Wine Windows taskbar was displayed over the top of the game until I clicked around on it.
The middle two winecfg options "Allow the window manager to decorate/control the windows" made no difference regardless of being enabled or disabled.
I also tested wine + wine-staging (minus the bad patch) + d3d9 and the issue returned. In the winecfg Staging tab, disabling the "Enable Gallium Nine for better D3D9 graphic performance" and instead selecting the option "Enable CSMT for better graphic performance", I was able to get the game working correctly again. Certainly not as good as using the d3d9 patch set, but better than nothing.
I should note that before I retested the above, I had replaced my RadeonHD 5870 graphics card with a Fury X. I doubt it made a difference as far as this bug report goes, but worth mentioning.