This may sound odd, but try changing this setting in your Serial object in your application:
RtsEnable =True
and try again.
I found the same issue on my (arg - Vista) machine, where it would work fine when talking with the Arduino serial monitor, but not my application. I created a simple print and receive set of apps, and they didnt work. I then updated the RtsEnable setting and amazed it started working.
Hope that helps