yes, that is right. I already thought that this was the problem, but than again i did doubt it because i anticipated that the arduino designers would have taken such a thing in account when designing it - so i gave up the thought on this being the problem.
You have both the GPS and PC connected to the same serial port, which means that the GPS is interfering with the PC<->Arduino communication. If you need to communicate with both the PC and GPS at the same time you must use SoftSerial for one of them.