That's an interesting problem you have - I had a similar experience with 12F629 where the chip behaved properly if all my timing was using PAUSE but failed to reprogram when using the NAP in my code... Finally I ended up using the extended temperature version of the device (12F629E/P instead of the I/P) and haven't had any problems since!
I had to use NAP to keep power consumption low - do you have a similar situation?
-warrier
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