What do you have your tare weight set to in osCommerce?
If you have this set to zero it would account for the discrepancies since once the product is packaged for shipping there is usually about 3 pounds of weight for shipping materials.
We use the following method to determine total order cost:
Product cost + $2.00 (handling fee) + rates determined by shipping method + sales tax (if applicable).
We currently offer the following shipping methods:
Free Local Delivery (as determined by zip code within a 15 mile radius)
UPS 2nd Business Day
USPS Priority Mail
All rates are determined by hooking into the UPS or USPS APIs over the internet and consider a 3 pound tare weight on all packages. Both API's use weight and distance shipped to determine a shipping fee.
In my state, sales tax is charged on shipping and handling as well as product if you are charging the customer a flat shipping fee. Since we are charging exactly what it costs to ship, we do not have to charge sales tax on the shipping. This saves our local customers (about 200 individuals) some money.