When you capture Anamorphic video the camera is set to normal 4:3 so there is no widescreen bit, to fix this, when the footage is in the bin, clik on it to select it, then open the file menu, select interpret footage and change the pixel aspect ratio to the proper one for your video format like 1.2 for DV NTSC.
I usually use Widescreen anamorphic lens on my projects for B-roll to mix with various flavors of HD, I use Scenalyzer to capture with as I can do two or three captures at once, and if the Scenalyzer capture is set to 16:9 it adds the WS bit to the footage.