You must take care with RTS signal, it's used to indicate to RS485 what is the way of communication (for example if you are transmiting or receiving). The problem is that in windows, cause it takes control of your system, when you transmit a data to your system, you put the RTS on, then when you finish transmiting you put the RTS off, but in windows it's not OK, it's not synchronize exactly when data is transfered (you cannot know when data is really transfered to RS485), it delays up to 10 msecs, so, the other system must wait almost 10msecs before it responses to windows packet... It delays all your transmition.