>> So what looks like is happening is;?
>> On programming, the EE values are all put in OK
>
>Sounds like they probably are

I would agree.

>> After a power down, the EE values 'leak'
>
>Very very very unlikely

Again I agree.

>> Doing a programmer READ 'refreshes' the values


No I suspect this fixes the bit of code that you are missing by resetting
bits that come up in a different state after power up.

what are you doing with the various bits in the EECON1 register?
Specifically the bits that swap between data, program and configuration
memory?

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