Yeah, it's a bit non-obvious. If I recall correctly, each mask is the seam 
between the blended image *so far* and the next input image.

So the first mask will be the seam between images 1 and 2, then the next 
mask is the seam between (1+2) and 3, then (1+2+3) and 4... and so on. If 
you can make sure your top-left most image is the first image, you may be 
more successful in overlaying them. Unfortunately, because of the 
sequential way enblend blends, it's possible to get counterintuitive things 
happening like seams crossing over each other.

Shameless plug, but <a href="http://horman.net/multiblend/";>multiblend</a> 
exists partly to remedy that deficiency (see "Consistent and integrated 
seaming").

It's also able to save out a single seam map, which can be easily overlaid 
onto the result. The one thing (okay, just the main thing) it *doesn't* do 
is optimise seams.

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