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Very strange, I haven't had that problem so I can't advise on it but you could try emailing Einscan support.
They were very quick to reply to another issue I had.

So the auto alignment in free scan isn't working for you ?
If so, have you tried manual alignment by selecting 3 points on the scan ?
I sometimes find auto alignment doesn't work in free scan with...

it seems to be an intermittent error in the calibration.
Try closing the program then start it again and recalibrate. That's how I get it to work again when it happens.

If that doesn't work for you, send Einscan support an email.
They replied to me very quicky last week with a fix to another issue I had.

Ok, I seem to have fixed it !
I uninstalled both version and reinstalled 2.0 by itself and autoscan alignment is working again. :)
I guess it's not a good idea to have 2 versions of the same...

Strangely enough, manual alignment works fine with mine. Can't understand why the autoscan alignment is so far out ???

I've been using the new v2.0 update of the scanning software for the past few days without any problems but all of a sudden, it seems to have developed a problem with alignment in turntable mode....