Thanks for the report.
Can you say which version of KStars you're using? Is it a recent release, or is it the "latest software" post release?
I have made substantial changes to the Polar Alignment system since the 3.5.1 release
e.g. see
indilib.org/forum/general/8602-new-polar....html?start=84#66910
so if you're using software from before that change (which is not in any official release), you may want to try the latest code.
If you're using my new version, I'd like to see a log. Can you provide a log with align debugging enabled?
On way to find out if you're not sure is to look at the main KStars SkyMap, and click "Help" --> "About KStars".
If it looks something like the image below (saying 3.5.2 Beta) then you may be using my new software,
if it says something like 3.5.1 or previous, you're not.
To answer your specific question, if you're using the new PA version, then it wouldn't matter if the scope you were using to capture the
PAA alignment images was aligned with your imaging scope or not, as long as they shared the same RA axis.
With the previous software, it probably wouldn't matter if they were a little off, but probably would matter if they were, e.g. 12 degrees off.
Thanks,
Hy