Got word from Microchip technical support. It seems that the problem could be with pk2, the command line software that's responsible for communicating between my computer to the PIC microcontroller in Linux. So Bill has a strong point there. I think what happened with the PICKIT 2 software from Microchip was that I didn't connect some of the pins properly, resulting in a program freeze. Other than that, I just found that that flasher software was resource-consuming, hence the reason of doing so in Linux instead. I will further look into pk2 and sdcc before I make the switch again to developing the control code in Windows. Thanks for your help.