Inconsistant alpha channel import on .mov files

Question

I am creating a movie using animation I create in Maya which is then composed in Shake with some alpha masks and exported using the animation codec to a .mov file into Motion. In reviewing my workflow (I'm about midway through things) I recognized I had an error in my screen sizes from one tool to the next and while it was not too noticeable, I thought it best to correct. This is where I should have left dead dogs lie.....
Anyway, this is best described with the flow I show below:
Motion Project Setup on ALL file types
720x480, 8bit, NTSC D1/DV
Lower First (Even)
29.97 Fps
Background Color - Black
Background - Transparent
Case 1:
Maya__->_Shake___->Anim Codec_________>Motion 720x480
720x486->720x486-->_Mil+_Col-->foo.mov-->File squished 6 pixels in Y
but alpha is present
Case 2:
720x480->720x480-->_Mil+_Col-->foo2.mov->File is 8 pixels narrow in X
alpha channel is not preset
I open foo.mov and foo2.mov in shake and look at the files and the
size is as follows:
foo.mov - 720x486
foo2.mov - 720x480
BOTH .mov files have the alpha channel present and the data is correct.
Just for grins, I output a file sequence of .tif files from shake of the
foo2.mov files and verified that the alpha channel was present in
photoshop and then did an import into motion with the same results of
foo2.mov. Size is shrunk by 8 pixels in X and no alpha channel.
It appears at least that Motion is making decisions based upon the screen
size and importing or not importing the alpha channel.
Any thoughts would be very much appreciated.

Answer 1

Well, it is strange. Shake says it is 720 and for that matter so does Motion in the Media tab. Motion says it is 720x480 as does shake but when the clip is overlayed against the black background you can see 4 pixels on each side of the clip. The motion project file says it is 720x480 too.
UPDATE....
I just checked the motion file and deleted all of the media clips, but when I went to the media tab there was still one copy of the old 720x486 clip there. Every time and method I tried to delete it, it would crash motion. So, I copied all of the other text data I was using motion to generate, created a new motion project and pasted the text in. When I import the 720x480 file into the new project it lines up perfect. This must be a "feature mode" I must have gotten motion into.
Anyway, problem solved. Thanks much for your help Andy. I kept looking at this and not seeing the forest for the trees.
Much appreciated.