I'm not seeing a difference when viewing the print previews in both v2 and v3. Maybe I'm missing something but if you could provide more details like a screencast of the differences please post here.
Or you can always reach out direct support (live chat) under Business Catalyst for quicker assistance here.
The print previews look fine for me as well, but when I print the V3 invoice, I get the complete screen shot similar to what you have included above, ie the side navigation is printed and the Preview box is printed over the top of the details screen.
The V2 invoice is printed correctly, as per the print preview.
I also printed in both interfaces but I'm seeing this fine on my end.
This could be something local...try saving your current invoice layout html code on your local machine than restore to default to see if this has any effect.
If no luck please reach out to our direct support via live chat or submitting a case with your site details to investigate further.
Actually Jim I was informed that it's actually a bug found in IE browser. If you use another browser like Firefox, Chrome, etc it'll work just fine.
This will be fixed in our upcoming release at the end of the month.
Hope this helps!