You are very likely wasting your time looking for a system issue when there is a 99% chance it is a user mistake. First you need to run account balance reports and find where the divergence is between the GL balance and the report. Once you know where the problem starts, run the End Period Wizard again for that month. Your accounts should then balance again. Of course, there could be multiple problems in multiple months, in which case you might want to spend a little time and re-run the End Period Wizard for each month of the year. If there is still a divergence, check your opening balance at the start of the year. You may need to adjust your opening balance in your GL to bring it back in line in a worst case scenario.
Once you're balanced again we recommend you place time based security restrictions on user security profiles, so users are limited in how far back in time they can change transactions. Also once a month has been finalised, you should go into the GL and lock the month so users don't change earlier transactions inadvertently.
What is a "costing allocation" ?-