Unwrapping ignores seams in very simple case
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I appended an example file i unwrapped a cube after marking every edge as seam. Somehow the bottom left and center left face inside the UV-Editor are connected, even so they are separated by a seam.

Steps from the beginning:
1. Open default scene
2. Mark every edge of the cube as seam (Ctrl+E -> Mark Seam)
3. Unwrap the cube (U -> Unwrap)
4. Inspect the result. Two supposed to be isles are connected.

r51276, Ubuntu 12.04, 64 bit.



The seams are not really ignored, there is just no gap between the islands, so they happen to be connected after packing the separate faces into the image. There is no explicit UV connectivity for editing, it's all based on UVs being in the same location. I've changed the default margin for packing from 0.0 to 0.001 now, which should keep them separated.