Hi Martin, the warning is from ilink it seems, which doesn't seem to handle WINDOWCOMPAT or doesn't like how it is being called. From the Tools Reference from the toolkit,
If <apptype> is given, it defines the type of application:
WINDOWAPI
Presentation Manager* application. The application uses the API provided by the Presentation Manager and must be executed in the Presentation Manager environment.
WINDOWCOMPAT
Application compatible with Presentation Manager. The application can run inside the Presentation Manager, or it can run in a separate screen group. An application can be of this type if it uses the proper subset of OS/2 video, keyboard, and mouse functions supported in the Presentation Manager applications.
NOTWINDOWCOMPAT
Application that is not compatible with the Presentation Manager and must operate in a separate screen group from the Presentation Manager.
OK, looking at the error LNK4072, it means
L4072 changing application type from oldname to newname
Explanation: The application type specified with /PMTYPE is different from that in .DEF file. LINK386 is using the application type indicated.
Action: Edit the file and relink.
So somewhere there are conflicts between WINDOWAPI and WINDOWCOMPAT, possibly it is emxomfld causing it but search your source for both.