The only other thought I have right now is to make sure that in SalesAnalysis, the option to retrieve taxes is still enabled. This can be found in the SA company profile. You can choose to turn off retrieving either or both Taxes and Misc Charges. This would influence the SA statistics.

If it was disabled by mistake, you may be able to fix this by turning it on, archiving all transactions for invoices and CNs still in OE current and history (by date range), and then running Scan Data from Other Systems to bring back the invoices/CNs with the taxes.