I have a door (two func_brushs that are parented to func_tracktrains that, when triggered, move apart in opposite directions) that is in front of a linked_portal door in a 128x128 square and the linked_portal_door is 56width by 56length as is the corresponding partner. When I move the linked_portal_door out of the door it is fine but behind it it doesn't work.

Here is a pic of the door http://imageshack.us/f/221/image1spl.png/
Here is the inside with the 2 door pieces deleted http://imageshack.us/f/440/image2tk.png/
(the purple INVIS texture boxes are the func_tracktrains)

The linked_portal_door connects to a doorway that has the exact same dimensions but is on the ceiling or floor, neither has worked.

Is your linked_portal_door open when the door opens?
Does both worldportals have a name, and are they both linked to each other?

Both doors are linked, (door1 -> door2) (door2 -> door1) and both are automatically active.

And there's a purple link line, when the linked_portal_doors are not behind the func_brushes they work fine, but behind them they don't.

EDIT: Turns out the linked_portal_doors work in game behind the func_brushes, but when my func_brushes move they wipe the world portals away forever in the map.. Don't know why, some annoying bug?

Got it, just changed the solidity of the func_brushes to 'Never Solid'.

doesn't that screw up the fact that they're blocking the worldportals?
What happens if you move the worldportals 2 pixels down?

I noclipped behind the func_brushes in game before they opened and the world portals were linked, but once triggered and the func_brushes moved, they would terminate the world portals link for some reason, but this doesn't happen if the func_brushes are never solid.