What I expected to happen was...:
When using /fill <x1> <y1> <z1> <x2> <y2> <z2> portal or /fill <x1> <y1> <z1> <x2> <y2> <z2> portal 0 or /fill <x1> <y1> <z1> <x2> <y2> <z2> portal 1, the nether portal blocks would be placed.
What actually happened was...:
In all cases, instead of the portal block being placed, a block of air was placed.
Steps to Reproduce:
1. Make a 3x3x3 area of air(works with any area as well)
2. Place any solid block below it.
3. Place any solid blocks around it.
4. Use the/fill <x1> <y1> <z1> <x2> <y2> <z2> portal or /fill <x1> <y1> <z1> <x2> <y2> <z2> portal 0 or /fill <x1> <y1> <z1> <x2> <y2> <z2> portal 1 (specify the area of air that you made)
http://www.minecraftwiki.net/wiki/Technical_blocks#Nether_Portal :