OK. The problem seems to be resolved. Thank you for your attempts to help. Here is the reply from Mr. Capps:

"The problem ended up being an obscure Perl issue -- we told it to join together an array, and it decided to randomly drop elements of the array when they weren't defined, which was unexpected. This lead me to believe that we'd again mis-indexed the fields, thus the resulting confusion. (It's even more fun because the problem only happens on certain servers running certain Perl versions... sigh.)"

Glad to see that your problem is resolved. My Server is running pretty recent software (I keep the software updated myself) so I'm not running the magic combination to cause the behavior you are seeing.