Hi John.
To see thru the polar scope you have to turn the scope to see thru it so that is correct.
After polar alignment you can turn the scope back again.
What firmware are you running at the moment?
You can look it up by opening a webpage and type in 192.168.0.111 but you have to be connected to the mount with a laptop.
Open the page "sram/firmware" on the mainpage.
The latest firmware for non beta users is 23 October 2011 and that has good pointing.
I don't know if you are a member of the Gemini-II Yahoo group but here is a link to it.
http://tech.groups.yahoo.com/group/Gemini-II/
At the moment we are testing the latest Dec 14 main firmware and Dec 12 hand controller firmware.
Rene is busy implementing PEC so that will be tested soon.
After a polar alignment it is best to drift align to get a better alignment.
After you have build a model you just have to warm restart the next night if nothing has been moved and just sync on one star and off you go.
From your sig it looks like you are in Kinglake so that is not too far from me.
If you need any help i can come over and help you.
Martin.