bitman, the URL you provide actually does not mention black holes at all. It ends with the blunt statement that the "failures" were confirmed to be caused by interference
from the ship's own radio systems:
"After much trial and error and experimenting, we determined that the GPS signals were not being received on those particular headings only when a voice telephone call via Inmarsat A was being conducted "
There's nothing new, or specific to GPS, about that. Active transmitters have always created interference
in other electronic systems and considering that GPS is designed to work with an extremely weak signal--it is very easy to swamp out that signal.
Same reason that you'll see a "NO TWO WAY RADIOS" sign in any blasting zone, the wires can act as antennas and pick up enough power to set off the explosives.