The 'standard report' for top 20 customers is for sales only and does not include misc charges and taxes, regardless of what you have selected to retrieve in the Company Profile. If you do choose to retrieve either of these, this means that you can use Online Inquiry, or GridView or Crystal Reports, to get the totals by customer you are looking for.

Adagio SalesAnalysis has a Top 20 customer YTD inquiry already set up as one of the pre-defined samples - you could use this. Make sure that on the first screen, the choices to include all record types (line items, misc charges and taxes) are selected.

Also make sure that the number you are comparing from AR is not just the YTD invoices but also incorporates YTD credit notes, which also populate SalesAnalysis data if you process notes from OrderEntry.