While I would prefer an in-game fix to this issue, I have been able to find a workaround, but it requires using a utility called DxWnd.
1. Download the utility from this site:
https://sourceforge.net/projects/dxwnd/
2. Extract the RAR file (you may need to download a free extractor, do a google search.) The program does not have an installer, so no other installation is necessary. I suggest changing the name of the extracted folder to "DxWnd".
3. Within the folder, find the application called "dxwnd". In order for this fix to work, you will always need to open this application as an administrator, so right click on it and select Properties. On the Compatibility tab, check the option "Run this program as an administrator". Hit Apply, then OK.
4. Open the dxwnd application and from the Edit menu, select Add.
5. Fill in the boxes as follows, leaving the rest unchanged (or modify at your own risk lol):
- Name: Railroad Tycoon II (or whatever you want to call it.)
- Path: Insert the full path to where RT2_PLAT.EXE is located on your computer.
- X, Y, W, and H: X & Y are the coordinates of the upper right corner of the window (so set them to something like 50 and 50), and W & H are the width and height of the window. RT2 uses 800 x 600 or 1024 x 768 as native resolutions (depending on the in-game settings), so the best results will be had using one of those two. You can use larger values in a 4-to-3 ratio, but it will cause the graphics to be stretched to fit, making text appear muddled.
6. Click the Try button to make sure it works for you. Then click OK.
Now, whenever you want to play RT2 in windowed mode, open dxwnd (as an administrator) and double-click the icon called Railroad Tycoon II (or whatever you named it.)