In group registration the customized fields appear for each member AND at the billing address page. Thus the amount for the extra fields is doubled - resulting in wrong totals....
Sounds like you do not have things setup quite right. First, are you using the latest release? If not, you need to do that first.
In Event Management you mark which custom fields are to be used for each event. To the right you will see group registration options. For each field, you need to mark if you want it to show on the page for each member, only the billing page, or BOTH. You must have it on both.