I had the same problem.
I purchased my pcDunino3B from Jaycar (in Sydney) but it had the LVDS kernel installed which means the HDMI output does not work.
Powering on the board showed NOTHING except a blinking LED (actually thought board was dead).
To use the HDMI output, I had to install a NON-LVDS kernel.
From the 3B page (http://www.linksprit...nano-pcduino3b/), I burned the "Ubuntu NAND Image ... 12-5-2014" listed at the top, then the "Ubunto 12-28-2015" OS. The board booted but attempts to do anything returned errors. apt-get update failed with errors you report.
Solution for me:
Go to the bottom of the page "Ubuntu 14" section. Burn kernel and OS from "https://s3.amazonaws...0141231.tar.gz"
Image from http://www.linksprit...e-for-pcduino3/ " Ubuntu 14" section also works (https://s3.amazonaws...AC_20150107.zip) but is for pcDuino3 instead. I don't know what the differences are.
WARNING: The file size is now about 1.5GB (kernel & OS combined) and PhoenixCard takes a long time to Burn the SD card. Just wait for it to finish (approx 5-8 minutes).
Hopes this helps.