The most common reason I found for the Standard I/O window to appear is the use of the printf function. I use it sometimes for debugging purposes, but this leads to the window to appear in the EXE even if the 'bring standard I/O window to front whenever modified' in the environment options is not selected. Check in your program if you have some printf statement left and comment them out, then recompile the project.
A more elegant solution is to condition those printf statements to the result of InStandaloneExecutable() function, to display them only in the IDE environment and not in the EXE program.
Roberto