We use this windowed mode from knxrb a lot and it works for us, although we're currently running FPSC v1.17 and no mods.
When we build our game, we put the EXE he provided in the folder with our game's EXE, and the windowed.txt file goes in the Files folder of the build game (along with an image of the icon we want in the window's corner). You may need to check to ensure you have done the same setup.
The readme also tells what the settings are for the windowed.txt file.
ADDED: Taken from knxrb's first post in the thread for this applet:
Quote: "It has been tested with the Stock FPSC exe but I've been unable to test it with mods yet (other than Horror Mod), so you guys will have to let me know how it goes with those"
You might want to take your question to the Wasp Mod thread and ask the developers there.

Twitter: @NFoxMedia