As per http://www.raspberrypi.org/phpBB3/viewtopic.php?f=28&t=13430&p=140906&hilit=6+flashes+led#p140906
3 flashes: loader.bin not found
4 flashes: loader.bin not launched
5 flashes: start.elf not found
6 flashes: start.elf not launched
So rpi-update is causing a problem with start.elf
The problem can be fixed by putting the SD card into a PC and renaming start.elf to oldstart.elf and then copying arm128_start.elf (or one of the other elf binaries) as start.elf