I am running into this myself. My profile views are 10' hor. and 2' ver. My drawing scale is set to 1"=10' and when I switch it to 1"=20' things change. But when I am in paperspace, no matter what I do, unless my viewport scale is at 1"=20', the items I drew in by hand are shifted. My original drawing scale was 1"=20' when I started the project. There is something up with the whole drawing scale vs profile view scale vs viewport scale. I just dont know what.
Still no fix in 2013. This issue has been around for a while. PLEASE FIX IT AUTODESK. Fortuantely Batch Plot corrects it before printing, otherwise I would have been making a bigger issue out of this.
Go to the output tab and select batch plot. Create your file list and then save it (optional). It should be intuitive enough to figure out from there. If not, read the help on it.
Well, that didnt work either. Set my viewport scale to 1"=20' and did a regen. Looks fine. Reset the viewport scale to 1"=10', didnt regen and batch plotted but the hand drawn items still come out shifted to the right by 5'. I can manually move things in my profile view 5' to the left to remedy this but what a dangerous way to do design work.
I am pretty sure my drawing scale on the settings tab was originally set to 1"=20' when I started this project. Why is it when my viewport scale is 1"=20' everything works fine? Real freakin nice Autodesk.
I finally got this submitted to the Autodesk developement and they're working on it. How long it will take to fix it, who knows. There is one thing to check that usually solves the issue.
In your profile view styles, check the right and left "axis offset" settings.(see attached pic)
If those settings are set to "0", for us at least that usually fixes the problem.
It means revising any profile view styles you may have set up, but if it fixes the problem, then I guess we live with it until Autodesk fixes it.
Win 7 Professional - 64-bit
Xeon W3550 @ 3.07Ghz
8GB of RAM
Nvidia Quadro FX 3800