The TopOff and Fast Charge safety timers are completely separate and do not affect each other. The minimum safety timer period is 3 hours from start of entering Constant-Current state. The fast-charge safety timer is for stopping the charger if it is taking too long to charge the battery (it is spending too much time in the constant-current state. This may be a sign of a bad battery if it is taking too long to charge).
Try the following to start:
Read back the CNFG_CHG_C and CNFG_CHG_E registers to double check the TopOff and fast-charge safety timers were configured correctly
Log the STAT_CHG_A, STAT_CHG_B, and INT_CHG registers for faults
If possible, repeat the experiment with one of our EVKits charging the battery to see if the same behavior occurs.