>So either I am missing something very obvious

Well, you are definitely doing that.

>OR something has indeed changed and the datasheet
>needs updating. Imho.

IMNSHO the data sheet is correct. As someone else pointed out, you are 
looking at ABSOLUTE MAXIMUM ratings, NOT operating ratings.

The current rating for the diodes allows static discharge during handling - 
not current while operating. These diodes are not specific components put 
there for the purpose you are attempting to use them for, but intrinsic to 
the manufacturing process, and made to have specific characteristics that 
allow them to become protection against static charges during handling. As 
such they have connections to "funny places" elsewhere in the chip 
substrate, and as you observe, when the diode conducts it does other funny 
things to the circuit which stops it working.

In short, despite other chips "apparently" working correctly, you cannot 
rely on this, and must use an external schottky diode to protect the input 
and stop the internal diode from conducting. Your talk of using a more 
expensive component to protect a cheap microprocessor is not an uncommon 
occurrence.

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