Btw. are the internal pullups, once activated by "pinMode(x, INPUT_PULLUP);" reseted after uploading a new sketch? I know auto-deactivating is now (IDE >= 1.0.1) done by explicitly setting the pin in the same sketch to output (see last paragraph Arduino IDE 1.0.1 – New Features « Adafruit Industries – Makers, hackers, artists, designers and engineers!). But what is happening after uploading a new sketch? I assume they are deactivated but I'm not a deep Atmel guy so I will not count on Guessing. 