My first thought is that the output projection needs to be the same as the 
input projection. Hugin defaults to equirectangular output, this will appear 
distorted if your input images are rectilinear.

Secondly, check that both your images have been assigned as a different 'lens'. 
This should happen automatically, but Hugin will assume they are from the same 
lens/camera if the image dimensions are the same and there is no other metadata 
found inside the file.

-- 
Bruno


On 16 December 2017 02:46:49 GMT+00:00, J Harvey wrote:
>I'm sorry not to get back to you.
>
>I've been using the gui because the two images don't have machine 
>identifiable correlative points.  (think images of the same scene, but 
>acquired non contemporaneously).  I've been using the same gui settings
>as 
>the command line, with customized control points, and I get two warped 
>images as output.
>
>On Thursday, November 16, 2017 at 10:37:04 AM UTC+1, Bruno Postle
>wrote:
>>
>> This is how it is supposed to work, the first output image should be
>the 
>> same as the first input image. What parameters are you using? This
>should 
>> just work: 
>>
>>   align_image_stack -a output 1.jpg 2.jpg 

-- 
A list of frequently asked questions is available at: 
http://wiki.panotools.org/Hugin_FAQ
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