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I have to admit that I'm not sure what Microchip wanted to do with the PICkit 3 programmer, works worse than PICkit 2. It is possible that they wanted to increase the sale of devices, because it would be harder to clone by home hobbyst. And in all this they started to play a little more, and we get product result. Of course they are a serious company and this will be solved.
Please check that the circuit components are correct for the debugger to work correctly? Here are the guidelines:
- Do not use pull-ups on PGC/PGD – they will disrupt the voltage levels, since these lines have 4.7k pull-down resistors in the debugger.
- Do not use capacitors on PGC/PGD – they will prevent fast transitions on data and clock lines during programming and debug communications.
- Do not use capacitors on MCLR - they will prevent fast transitions of VPP. A simple pull-up resistor is generally sufficient.
- Do not use diodes on PGC/PGD – they will prevent bidirectional communication between the debugger and the target device.
in Mplabx window right click on your project folder and select Properties. Then choose the debugger as Pickit3. Also search on microchip forum related to this problem. I also have same problem but after reading some posts on microchip forum, i have fixed it. GoodLuck