Go to your item, go to the average cost field, press F6 to bring up the value entries, start filtering to start investigating. It should be pretty obvious if you have a negative average cost. You should also look at your BOM, run the detailed calculation report on your item - what is the total cost Navision expects?
As stated earlier you need to investigate the item ledger and value entries to uncover why they are negative - you simply need to look at the data and investigate it, not much anyone else can do here except dial in and look at your data - it is time for you to investigate the lines that make up the final cost and discover the reasons behind the values.