Calculating incorrect cost for Shipment Total Transit Time

Summary:

We have the rates based on shipment transit time and the process is as below.

We are creating shipment— Inititilly we are using look up rate service in RO and creating the shipment

Lets Say order

SOURCE: A
DESTINATION: B

Look up transit time : 6hr

then shipment gets created for A To B with the trasit time of 6hrs and cost calculating correct(lets say every 1 hr 100 $) as 600 $

Then when you assign fleet / insert mannual stop -happend we have NFR/Other got inserted which is lets say stop: X

Now stop: NFR to Pick up: A , the look up is 1 hr