Intercompany Invoice with ship from warehouse will not produce tax line

I am hoping someone here can help, please.  I have reviewed troubleshooting E-Business Tax notes, am currently running setup diagnotic script, and have had an SR open for 2 weeks with virtually no progress.  

Our problem is that certain Intercompany invoices are not calling E-Business Tax module and therefore not applying VAT tax at all. We have identified the difference as invoices that have a warehouse populated. I can reproduce the problem with two manual invoices: One, entered without a warehouse, calls E-Business Tax and applies VAT tax. The other, identical in every respect except that a warehouse is entered, does not call E-Business tax and does not apply VAT tax at all.  (not a $0 tax, but no tax line assigned at all to the invoice)