There are only three things I have seen that can cause this.
1st. Having the global replication throttle enabled and having the schedule replication enabled, the scheduled throttle will overwrite the global throttle.
2nd. Old firmware, specifically 2.1.3 and below.
3rd. 10/100 base NIC cards. If the NIC card is not at least 1 GB, the DXI is unable to use the throttle settings correctly.