There are a bunch of places this can go wrong.
 
First off, I'm assuming you've double checked that the items in question are marked as Taxable, that the Customer is set to Taxable, and the Tax Group assigned has Tax Code(s) with tax percentages...
 
Not calculated at all:
When you create a Quote, the Tax Group may not be pulled in. If you convert the Quote to an SO, there will be no tax. At one point the SO would not allow you to have the Tax Group Empty, that went away at some point.
 
Over/under estimated:
Not sure what you mean by "estimated", but you cannot trust the summary on the SO screen if you change the quantity or price.
 
Taxes calculated but not shown:
This doesn't happen to be on the Acknowledgment, does it? Tax is not being charged on "Freight" on Acks, but is on invoices. If you had an invoice for just freight the Ack would show no tax,
 
HTH,