Hmmm, I think the likeliest problem here is (and I hesitate to say it....) have you done all 12 frames? Or did you manage to do one frame and then load it in 12 times with BIFReader?

If I'm working on unit texures I usually follow this procedure (all I've done is change shields and weapons so far, changes to the men are a lot more work ):

1) Open the BIF with BIFReader (use the HIGH resolution one, ie BIFName_H.bif))
2) Watch the full animation cycle using "Timer" - you can see if any apparent spaces in frame 1 get filled in elsewhere in the cycle (the "dying" animations are little beggars for this )
3) "Export ALL frames to BMP" - this saves the BMPs as BIFName_H_f1.bmp to BIFName_H_f12.bmp
4) Open up BIFName_H_f1.bmp in Photoshop
5) SAVE the colour table (usually as BIFName.act) - you might need this later
6) Edit frame 1 (add in weapons, redraw shields etc) making sure it's all in space that is free in all 12 frames
7) If you need to go into RGB colour at all, that's fine, so long as you go back to indexed using the saved colour table.
8) When frame 1 is finished, use the rectangular selection tool to copy the changes - preferably extending the selection to an edge, or better still a corner, of the frame, and making sure to avoid areas occupied by men in the other frames
9) Open up the remaining 11 frames. Make sure you have "Snap to grid" selected (I think Photoshop defaults to this, as I can't remember how I set it myself...)
10) Work through f2 to f12 and paste the selection into each frame - by using snap to grid you can drag it into position consistently (this I why it's best to extend it all the way to a corner, makes it very quick)
11) As each frame is finished, I usually SAVE (this gives an edited copy in the same file name) then RESIZE it for the low-res version (Image>Image Size - have proportions constrained and change to 256 pixels width/height) then SAVE AS, changing the name to BIFName_f1.bmp etc (ie remove the _H from the original file name).
12) When you have done this you will have BIFName_H_f1 to f12.bmp and BIFName_f1 to f12.bmp.
13) Go back to BIFReader and open a NEW BIF (512 x 512 pixels x12 frames) then IMPORT ALL FRAMES. Select BIFName_H_f1.bmp and click okay. It should tell you "12 frames loaded successfully".
14) Run the TIMER again, to check that your new weapon/shield is located consistently - if not it will jump around. If you're happy with the result, save the BIF as BIFName_H.bif, then repeat with the low res version (256 x256 x12 frames, save as BIFName.bif)

From your description it sounds like you edited frame 1 only, then when you loaded back into BIFReader it copied the same one into all the frames.

Obviously, if you're making changes to the men, you will have to edit each frame individually - which is why it's a lot more work.

Hope that helps