Thanks for the answers. Hopefully, if standard peripherals sold by sparkfun don't work anymore, we can expect a fix rapidly.
As a note, i do not use the SMD version of uno. This, then, seems to indicate that at least it would not be due to a faulty CPU batch and that if there is a routing mistake, it has to be the same on both boards.
edit: By the way, it seems that pulling up non-PWM pins block the boot, while PWM pins don't. Any clue?