Some more about my issue. I tried an alternative calling irw direcly in my java code
p = Runtime.getRuntime().exec("irw");
And the result was exactly the same. Once the motor starts turning, the IR receiver seems hanging. When the motor stops, the IR receiver works again. Some reading and searching on the internet learned me that a possible cause could be electric noise because of the running DC motor. I tried to put a capacitor around the DC motor but without result. In other words I am stuck for the moment and thus still looking for a solution. If any of you would have any suggestions, they would be very welcome. I have no electronic background what probably explains my lack of knowledge on that.
In the meanwhile I also posted my issue on a Raspberry Pi forum. See Forum post
I will keep you posted as soon as I get around this issue.