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Microcontroller programming using universal programmer tool

I am using NXP P89LPC954 microcontroller(www.kynix.com/.../P89LPC954FA,529.html). I am having problem with In System programming(ISP). When i solder it on my board for the first time and try to burn hex file into it using phython chip prog, all the process i.e burning the hex file and verifying after burning, everything goes fine in the chip prog software. But the microcontroller does not behave as per the code.

When I burn the same hex file using "universal programmer"(De-soldered microcontroller inserted in the Device pins ) having parallel port, it works fine. Once the code is burnt using parallel port device, from next time onwards i'm able do the isp programming.

Actually i was told that we must dump any microcontroller for the first time using universal programmer only to make it compatible for isp. But what i feel is if that is the case then why not the manufacturer does that by default(As it is not user program dependent)

Is it required to program all microcontrollers for the first time using parallel port universal programmer only,to make it compatible for isp??

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