When you import accounts from multiple QIF files, each file represents a separate account and the transfers are imported to AceMoney twice (an outgoing transfer from one file and an incoming transfer from another file). Unfortunately there is no automatic solution to detect them, so you'll have to go through these transfers and remove the duplicates manually.
We understand that it's not an easy task, but unfortunately this is the only way to fix wrong balances. However it may not be that difficult if you follow these instructions.
Import the QIF for the first account, ensuring that it's imported to an account name that is identical to the original account name. Delete ALL transfers to or from this account (easy to do by sorting the account according to payee, shift click to select entire transfer range and delete).
Import second QIF. Delete ALL transfers to/from the second account EXCEPT those relating to the first account.
Import third QIF. Delete ALL transfers to/from the third account EXCEPT those relating to the first and second accounts.
Continue until all account are imported.