On the last couple of polycarbonate prints with my Prusa, one or more layers have been completely skipped (i.e. no material extruded). The rest of the print is fine save some minor warping. I'm printing in an enclosure that gets up to ~60 °C with the power supply outside the enclosure. I'm also printing out of a dry box with a fairly long bowden tube. I suspect it has something to do with overheating because this doesn't happen when I print without an enclosure.
If you are experiencing overheating, consider to provide input/output airflow to the enclosure for the controller board and for the power supply. I've seen elsewhere on the 'net (forgotten locations) of Prusa printers with DIY extensions to the cables that are used in those components, allowing them to be located outside, with ambient airflow.