When work orders close with a negative variation, that means that transfers to finished production out of work in process, exceeded the dollar value of work in process for that job.  
 
Are you responding "YES" to the question "Is this the final quantity for this work order" when the last entry to finished goods is made?  
 
By answering YES, EVO will true up the dollars to finished production to equal total dollar job costs on the last transfer to finished goods.
 
The $.01 entries are just rounding differences.
 
If you run EVO report JC-M, you can readily see the total job cost of a work order, the dollar value of transfers to finished goods to date, and the last column represents the difference, whether positive or negative.  If you see a negative in the last column, you may consider overriding EVO average cost calculation when entering transfers to finished production.  
 
Hope this helps, neighbor.
 
Bensenville, IL

Not knowing if you are using Average or Standard costing methods -  
 
If you are using standard cost method for entering partial transfers to finished goods, the last transfer to finished goods entry should be coded as "N" (partials should be coded as "Y").  You can check this by going to WO-I, enter finished production, and click on the bottom button called LOOKUP.  Under the top column labeled "S" for standard, there should be a "N" for last entry in order for the system to true up to actual costs.
 
If you are using the Average Cost method, all transfers to finished production are coded as "N" so I do not know of any way of knowing for sure if the data input clerk selected "Y" for final transfer to finished goods.
 
However, you also can look up the part number in IN-E, and subtotal all transactions to finiished goods for that work order.  If this total is different from the total job costs, that indicates a problem with the last entry to finished goods.