I'm sorry, I know "
it works for me"
is unhelpful, but I'm not sure what's going wrong. I didn't need to edit any files to make it work, and SubTerra.exe runs without any compatibility options set.
Just in case, I've gone ahead and uploaded this full working copy of SubTerra. (I hope that's not a problem with the Crystal Shard folks, since the game's free. Please PM me if you want me to take it down!)
https://mega.nz/#!hhhHHAKB!p6wFC6nEDYf5X7r7ycxvKFno_78OfVXczNnZnYj4umU
If you replace the contents of your SubTerra installation folder with what's in this zip file, it should hopefully run. It contains just the required DLL files from WineD3D: ddraw, libwine, wined3d. I also went ahead and followed the hex-editing directions from that other WineD3D build: ddraw.dll is renamed to ddsub.dll, and the reference to ddraw.dll in SubTerra.exe was changed accordingly. Again, it worked for me without that step, but I thought it was worth a try in case there's some odd compatibility issue. I've tested this copy of SubTerra on my 64-bit Windows 10 PC, and it runs at full speed without crashing.
There's another graphics compatibility tool that might be useful:
dgVoodoo2. It's a few more steps to set up than WineD3D usually is, but I just tried it and it seems to work about as well. Here's the process, starting from a clean installation of SubTerra (with the original SubTerra.exe, no compatibility modes set, and no extra .dll files in the folder):
1. From the dgVoodoo2 zip file, copy dgVoodooCpl.exe and the DLL files from the MS folder to the SubTerra install folder. All files should be in the same folder as SubTerra.exe, don't leave the DLLs in a separate MS folder.
2. Right-click dgVooDooCpl and run it as an administrator.
3. Click the button near the top-right that says "
.\"
. That will tell dgVoodoo to make a local configuration file just for this game.
4. In the general tab, set the scaling mode to "
Stretched, keep Aspect Ratio"
. By default it seems to stretch the image to fill the entire screen, so it would be distorted on wide-screen monitors.
5. In the DirectX tab, disable the dgVoodoo watermark.
6. Click apply, close the control panel, and find out if the game works.