Nemesis,
How is the HSWAP_EN pin connected? This enables/disables the internal weak pullups while configuring.
If the weak pullup is not enabled, then the pin is tristate while powering ON.
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Table 1.1, note 2 page 14; and Table 1.2 page 15.
In any case, the IO pins always have their intrinsic diodes internally:
gnd-------->|--------IO pin------>|------Vcco
So, the pin voltage can not be much less than ground, and not much more than Vcco, as then these diodes are forward biased, and the pin is clamped +/- diode drop from ground (for negative voltages) and Vcco (for voltages greater than Vcco).
Since you seem to have the problem that the pin is going high while configuring, it is not anything to do with the diodes.
A pulldown resistor, once the IOs are set to be tristate while configuring, is the probably answer. The IO pin leakage worst case is
10uA, so if there is no other leakage, the pulldown could be something like 10K or 100K ohms, and be sufficient.
Even a very weak LVCMOS IO standard should be able to pull up 10K to the Vcco rail.
Austin