Do Processing Rules effect Data Warehouse? I once had a processing rule which filtered out all numeric digits from all clicks. We created this rule to avoid collecting account numbers (PII). This processing rule worked as designed as no numeric digits appeared in UI data. I was horrified to find account numbers in Data Warehouse as Data Warehouse ignored my processing rules.
Now that I think about it, Data Warehouse must be available only after processing, since it includes values that are only set during processing (e.g. context data). It seems most likely that the conditional rule is failing. You may also want to do a Data Feed export on the variable(s) in question to compare the pre/post variable values to see how they were processed and if things are making it past the filtering processing rule.