When an employee is paid multiple earning types that have varying taxability (for example, bonus, lump sum, pay in lieu) on the same additional check, and on that same check there is a pre-tax deduction for an RRSP, the application only applies the RRSP relief to the bonus earnings on the check. This means if the RRSP amount exceeds the bonus amount that is intended to be applied against the other earning types (like lump sum), there will be no tax relief on those non-bonus amounts.
As a best practice, you should enter multiple earning types such as a bonus, lump sum, and pay in lieu on their own check, and add the applicable amount of the RRSP to each of the checks. This will prevent the loss of tax relief in situations where the RRSP is greater than any one of the single earning types being paid.