Exception Time for Full Pay Period Shorting Employees Pay

We recently had an issue with our payroll for salary semi-monthly employees that received pay increases and had exception time in the previous payroll.  We pay current with exception time in a pay period lag.  The current pay period had 80 hours of work time. 80 hours of exception time was reported in the previous payroll. Normally it would be fine to zero out REG, instead of offsetting, as it matches the pay period hours. This was delivered I believe in 15-C.  However, the current pay period had a pay increase, so when it zeroed out REG (offsetting it), it