Usually the problem you reported is caused by non-common property/properties existing in symbols cached in schematic database. To confirm this please select one 'problematic' symbol instance in the schematic, select BOM property in Properties window and check details printed at the bottom of this window. Do you see 'Non-Common Property' string?
Thank you in advance.
Shortly after I posted this, I noticed that the property fields labelled non-common were the ones that were missing from the partslister output. I ran the script that mentor provides to delete non common properties and replace them with common ones, and now everything works fine.