Sorry for the delay.  The e-bots seem to be rebelling lately.  Perhaps I need to clear my AOL cache, as instructed on the Rosity front page.  Hmm.

The two meshes you're comparing have the same shape, correct?  You altered the vertex and polygon structure without changing the countours, as it were.  Hmm.  I've not yet encountered a situation where two identically-shaped meshes caused trouble.  And the error you get is simply that the script seems to stop responding?  How long have you let it run, in any given case, before bailing out?  And it may not make much difference, but what version of Poser are you using for this? 

Are you lining up the heads in the 3D view before running the script?  You shouldn't have to do that, I suppose, if the shapes are the same.  A common problem people have had is failing to align the meshes as well as popssible before comparing them.

Step-by-step, what is the process you are applying?  I know that's a broad question, but I'm kind of groping for an explanation, now.  I don't know enough about what you're encountering to know what else to suggest.

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Cage can be an opinionated jerk who posts without thinking.  He apologizes for this.  He's honestly not trying to be a turkeyhead.

Cage had some freebies, compatible with Poser 11 and below.  His Python scripts were saved at archive.org, along with the rest of the Morphography site, where they were hosted.