Mohamed,
On the Manual Shipping Plugin:
I removed everything from the RESTRICTIONS except for Zone = 'None' and Currency = '$USD' and it added the $5.00 shipping. I added the 'Headland' warehouse and it added the $5.00 shipping. I set the Zone to 'United States of America' and it added the $5.00 shipping. Note: I had set the Override shipping address to 'Your shop address'. I put in a price restriction of '0' minimum and '99.99' maximum and on a $29.99 order, it added the $5.00 shipping but on a $102.99 Sub-total order, it still added the $5.00 shipping. Note: the Use Price per product is set to 'No'. On the $102.99 order, I removed an $18.00 order and it retained the shipping. However, on the $102.99 order, I removed the $84.99 item and it removed the shipping showing a subtotal only for the $18.00 item. Finally, I added a quantity of 2 for a $49.99 item which was a subtotal of $99.98 but it did not add the shipping.
So it is working now except it is charging shipping on orders over $99.99, it is removing shipping on 'certain' item deletions from the Checkout page and it is NOT charging shipping on a $99.98 order even though the maximum is 99.99.
Any ideas why it is does this?