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AM335x with pullups on external power

I am working with a BeagleBone/Cape style design.  I have a power supply on my Cape to generate +5 and +3.3
for local hardware.  I am feeding the local +5 to the BeagleBone to provide it's power.  
My concern is that I have to put some pullups on some I/O pins to prevent my hardware from doing bad
things until the processor initializes the I/O.
Since the power on the Cape will be powering the BeagleBone,
the pullups and some of the Cape signals to the BeagleBone will be present before it powers up.
Does this present a problem to the i/o pins on the AM335x?

Gerry Belanger