Ashish, i've few questions against your query.
1. What's the Calculat.type for your freight condition type?
2. In VTFL for your item category what's the pricing type there?
3. What's the condition control for 2nd line item?
4. Is the freight condition manual or automatic and is the condition type is same for both line items?
5. Any enhancement has been done on sales order (trigger point save) for updating new pricing?
Lastly, if possible can you please share the snapshots of customizing settings so that the values can be identified. Thanks.