Ok, then back to your first example where you said you had the problem... what in that, if any is tax exempt? Impossible to help without complete info :)
I'm presuming it is all tax exempt? That's why GST and GST+PST are the same. Still, it is obviously not calculating correctly:
[qoute]Sub-Total: $31.85
Store Pickup (Walk In): $0.00
5% GST # 86028 4694 RT0001: $3.58
8% PST in Ontario + 5% GST # 86028 4694 RT0001: $3.58
Total: $39.02 [/quote]
On $31.85, GST would be $1.59 not $3.58. So your GST is effectively calculating at aproximately 11% and I have no idea what you could have entered to achieve that! Your 8%+5% is also calculating at 11% for an total effective tax rate of around 22 and a half percent.
You clearly have some settings messed up. Is this a production site? If not, perhaps PM me your admin info (address + login + password) and I can take a look.