data sent on serial connection from PC on boot

When I boot up my computer with my Arduino connected via USB I can see the TX and RX LEDs light up for several seconds. The PC is must be sending some junk data to the Arduino at that point.

The problem is that when the computer has fully booted I can't communicate with the Arduino. It's like the program on it has stopped running. After pressing the reset button everything works fine again.

My project requires the Arduino to be on all the time. When my PC is on I want to be able to control it manually and when not it should operate autonomously. This is not currently possible because I keep having to press the reset button.

Has anyone seen anything like this before? Does anyone have any suggestions?

My Arduino is a Freeduino 1.16 with Atmega 328. My computer is running Vista with a Gigabyte motherboard.

When the USB reestablishes connection it resets the arduino, it hen looks for serial data and thinks it is down loading data but non even comes. To stop this remove the auto reset circuit on the arduino. This might mean un soldering a capacitor into the reset line. See you arduino's schematic.