First SYFY ordered half a dozen episodes for season 6 of Eureka, then they cancelled the show with the Season 5.
Now, SYFY has ordered one more episode, an extra hour to 13th episode (the finale), that will give the writers an oppurtunity to wrap the show up.
Apparently, season five was to end on an cliff-hanger so SYFY went ahead and green lit an extra hour.
Source: EW