If the problem is offsetting transactions, you can also use the Create Write-off Batch function under Maintenance. Ask it to writeoff Balances between -.01 and .01. It will create a batch of adjustments.
Looking at the batch you will see each positive transaction followed by a negative one for the same amount. Unless you have some whose balances were .01, the total of the batch will be zero.
You can edit the batch to delete anything you do not want to include, then post it.