Humn, is it a Windows app? (as opposed to a DOS app which may/may not work as expected - it's been a long while since I wrote a driver to allow a 16 bit DOS app access to a 32 bit driver - I can't even remember what they're called now)

If it's a Windows app (and it's using CreateFile rather than trying to write directly to the IO port using asembler) and long as there's no specific timing that needs to be achieved then I'd expect a USB serial port to work correctly, Microsoft CDC bugs excepted unless you go for something based around an FTDI chip.

May be worth exploring first.