HugoPT:
The reason is very simple.You can't open serial port at VB and simultaneously on arduino IDE!
This true, but doesn't seem to be the OPs problem is he has accurately stated his process in Reply #17
There is no difficulty (on my Linux netbook) having the Arduino IDE open and able to upload sketches while at the same time running a JRuby or Python program that communicates with the Arduino. Of course I must complete the upload (or close the Arduino Serial Monitor) before trying to use the JRuby program, and vice versa.
As I have tried to show in Reply #18 I think the OP needs to reorganize the order in which things happen.
...R