Well I still don't have a "fix", or even any messages in the logs to account for this behavior, but every software release I'm having problems with is one where, when importing the installer, I told to update an existing resource (since a bulk of these software packages had already been picked up by full inventory scans and were listed in the "installed software",) instead of creating a new one.
That has proven to be a mistake, and I've posted a big note for all my colleagues to just create a new resource when importing packages