Hi Smiller
The fields should be grabbing the totals based on what Payroll Categories are linked to it.
I have seen a few cases where Salary Sacrifice has increased the W fields instead of decreasing which can cause the same problem you have reported. Could you check if this might be the same issue in your case?
Otherwise, what I recommend doing is running the Payroll Register [Detail] report as this will give you a full break down per-Category, then if you open the Online BAS page and go to: Settings > Set up activity statement fields, you can then check what Categories are associated to the W field and then check the figures accordingly. This can give you a much more in depth view if a specific category is throwing it out or the figures are all wrong.
Keep me posted on how you go.