The electromagnetic interaction between Io and Jupiter's magnetic field leads to single or multiple ultraviolet spots near the feet of the Io flux tube. Variations of spot numbers and brightness and of inter-spot distances have been observed to be linked to Io's position in its plasma torus. We have studied the evolution of the Io UV footprints with a time resolution of a few tens of seconds using the Space Telescope Imaging Spectrograph (STIS) in time-tag mode. We present evidence of systematic strong brightness variations of the main spots (up to 50%) with a typical growth time of 1 minute. Additionally, unanticipated simultaneous fluctuations of both primary and secondary spots have also been found in the southern hemisphere. Our findings suggest that the footprint brightness is not only actively controlled by the plasma directly interacting with Io but also by the poorly constrained electron acceleration region between Io and Jupiter.