FlexiTime allocates annual leave based on the Normal Hours per Week entered on the Setup > Employee screen under the Leave tab. If this field has a set number of hours e.g. 8 hours per week this will be used to accrue 32 hours per year (based on the default Holiday Rate of 8%).
If this field is left as 0 (zero) then the employee will accrue leave based on the actual number of hours paid. This is often the best setting for an employee who works variable hours. In this case the accrual will be 4/52 of the number of hours paid.