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G'day Chris
Have you tried with the BatchPreProcessing script to see if that at least gives better result in terms of alignment? Might help highlight where you're going differently?
Other suggestion would be to post some screenshots of each process settings, and maybe a few of the files, at least the one you're using for registration?
Another thought - are you sure the newer trial "_r" suffixed files are in fact newer. ie you haven't changed a setting where you're still actually looking at original poorly aligned subs, but you think you're looking at the output of further testing?
Sorry if you're tried the above, I'm not trying to tell you how to "suck eggs". Just some thoughts I'd try if it were me.
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