Many of us have the same problem. In my experience it seems to be related 
to Enblend blender.
Switching this to Verdandi ("builtin") option in the stitcher tab (advanced 
and expert modes) might help. The result will not be perfect; in my case 
there were often visible seams left over, but it generally changed the 
output.
Khan deghosting takes a f**kton of time; avoid it.

At the following link you can read about my latest conversation about this, 
and all the accompanying notes:
https://groups.google.com/forum/#!searchin/hugin-ptx/exr$20breaks%7Csort:date/hugin-ptx/b9qM0oQKZuk/mK6t9eTSCwAJ
I should note that what solved the issue then does not work in my latest 
batch. I believe it is due to high parralax more than .

For your case I would like to summarize two points:

   1. if the photometric calc returns too many grey values *(30+ stops)* 
   you will probably have black holes ("gaps" in my text). You should expect a 
   certain amount of EV levels and watch for breaches of that number. I have 
   noticed this usually influences the next point.
   2. if the stitching takes a long time or hangs at certain points the 
   panorama will probably be broken. Usually the worse it is the longer it 
   takes. Here it helps to look at the log output and expect relatively 
   regular progression in stitching and calculating new views. If it takes 30 
   minutes to calculate 1 picture you are either working for NASA or you can 
   press cancel. ← exaggeration, use your own metric.


I use a circular fisheye and make 5 views by 6-10 exposures for 
equirectangular exr output. In best cases the whole process took less than 
an hour including corrections.

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