RE: Penny Rounding Problem with Sales Tax on Sales Orders versus Sales Invoices
What is your setup in Sales Tax Areas setup for Rounding Tax? This could be due to Tax Rounding setup. Try different values of the setup. Alternatively, check values in "Amount Rounding Precision" in Currency Table for the currencies you are using.
Also, check Invoice Rounding in Sales&Receivables setup.
Also, there might be issues with partial shipments (I'm not sure that it is your case, but we have struggled with that quite a while). E.g., you can have a sales order for 10 items; when you post first five, the sales tax could have (e.g.) 0.254 in the end. Those would be rounded to 0.25 according to normal mathematical rules. Posting next 5 units will do the same - 0.254 but rounded to 0.25. In total this two shipments will give you a sales tax of 0.50.
However if you would look at the whole sales order, the amount of sales order for the whole 10 units would be 0.508, which would give in total 0,51 :-). Thus, if you had sent the invoice in advance, the customer could pay it and the difference appears. In this case there is not much you can do with the standard tools - one option is to make a customization and calculate if the partial shipment is actually the last one for the sales order and give a user warning message that the total amount of posted partial shipments would not be equal to the total of the sales order; in this case you can adjust the amount of the last posted shipment before the posting.