Shipping Calculation all screwed up after upgrade

I upgraded from 1.8 to 1.9 and the shipping is calculation wrong.

Like for instance: I have 0 to 1 lbs charge flat $1.5 per lb it comes up with $0.00, now when I enter $3 per lb, I get $1.50 I want.

For 2 to 3 lbs I have to enter $1.75 per pound to get $2 as the shipping amount, weird as hell?

What gives? something I did not do right?

I use to have 0 to 1 lbs charge $1.50 (worked great)
2 to 3 lbs charge $1 per pound and I'd get $2 if someone ordered 2 items (product all have 1 lbs on them)

ok so now I change it to fixed rate shipping of $3.50, and the site shows $2.00, how does it go from $3.5 to $2? My currency is USD???

OK, so it looks like after the upgrade, no matter what I use, by total, by weight, fixed and it does not matter what product. I am off $1.50, so if I make Fixed $5, my shipping is $3.50, etc

I got $1.50 "stuck" somewhere, any ideas what or where? I installed a FRESH 1.9 on a test url and the shipping works fine, so something is wrong when I upgraded...??

Thanks...

It seems that you have a discount applied to shipping...or your prices are displayed without tax (and you changed tax settings so prices are entered incuding tax)