I have seen this too.
It is as Gerald says. Your cape is loading one or more of the boot pins.
I did a cape - even though all the connections were high impedance inputs,
it was still enough to twitch the boot pins. Anyway, I ended up adjusting a couple
of the pullup resistors to adjust for it on the pins I was using - changed from 100k to
33k. Only had to do this for the pullups - so apparently stealing even a little from the
33uA max source was enough to impact the boot read of the pins.
Hope that helps.