Inconsistencies with Benefits Billing Enrollment and Arrears

We are experiencing inconsistencies with deductions for employees who are enrolled in Benefits Billing.  Some employees do not have deductions appearing as 'not taken' in paycheck data (as expected).  Some employees do have deductions appearing as 'not taken' in paycheck data that is putting the balances in arrears (unexpected behavior).  We have been unable to explain this inconsistency.  Has anyone else experienced this?  Both scenarios include employees in the same paygroup/benefit program/active Benefits Billing/on leave in job data.....identical except for the arrears issue.