This is for an order that has two taxing authorities (State and Local). The SO is being calculated correctly and showing the proper total on the SO the bottom of the SO screen, but the Tax printing on the Ack does not include tax on the freight. Further, when a "deposit" (payment in full) was applied it shows the SO total including the full tax, but when I print the Ack it shows a CREDIT amount equal to the total Tax on the Freight.
 
The tax group is set up with both tax codes charging tax on freight. Everything looks right except the Ack, and I know that you can't over-apply a deposit - it won't let you apply more than the SO total.
 
This is not a new tax group - we've been using it for several years and never encountered this issue before. The only thing I can think of is that originally there was no freight on the SO, so when I added it maybe something got messed up. I suspect that when the order is shipped and invoiced everything will come out ok, as we've had issues in the past where the Ack or Opening List total doesn't agree and it has. However, I can't really send a confirmation of deposit showing a credit balance as if we overstated the amount...

Turns out it's not the EN system and does seem to be consistent. I've reported it on the BugTracker.