I'm using Magento 1.4.2.
When I'm paying for an order with Paypal, the total is calculated alright but then Paypal charges twice for the shipment.
I'm not using any custom modules.
Any idea why this might be or where I should look?
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This is a rather old question but as I ran into the same issue with a customer today I'd thought I share the solution to this problem for future reference.
The solution is to disable the "Transfer Cart Line Items" option for the PayPal payment method you are using. By disabling this, Magento will no longer give details about the totals, tax and shipping to PayPal. It will simply tell PayPal to charge the customer for a single item (for which you can specify your own text under "Summary Text for Aggregated Cart") with a value of the total order amount.
The bug seems to be in Magento though and not in PayPal. I think it only occurs when your shipping fees do not include sales tax and Magento has to add the sales tax in the grand total.
Are you using Website Payments Standard?
Note: this doesn't apply if you use Express Checkout and/or Website Payments Pro