It has been observed that all bills or paid bills are showing as due at the time of receipt entry or in voucher entry. It can be seen in Alt-O:Outstanding report as well. Sometimes, bills are showing negative amount as double payment as well.
Please follow following steps from System->System Maintenance->Reposting menu.
1. Repost Invoices.
2. Repost Receipts
3. Repost PDC Receipts
4. Update Outstanding and Links
It is important to follow above steps in sequence. If you still face problem, most of the time you have to run above steps again. In some cases you may need to modify receipts and remove double entries of invoices. You have to check that while using bill wise receipts, you actually post payment against correct bills. If the payments are received on account, you need to be more careful while adjusting bills.
When you run Update outstanding option, it may ask for a password to delete links, you have to contact us to get the password. Generally it is not required, so it is locked. If you do not run option 1 and 2, then this question may appear but password should not be entered and option 1 and 2 must be run before running Update Outstanding and links.
If you are having day wise posting of sales bills, you can shift to bill wise posting using System->System Maintenance->Reposting->Change wholesale posting bill wise. If you are posting bills in salesman account in place of customer account, you will not be able to use this option. In this case, you can shift to bill wise posting option at the start of new financial year.