Thanks for providing the link.
Unfortunately I wasn't able to test Ninja Shadowbox for the reason that it is not activated on the page.
As far as I could inspect, the needed files for Ninja Shadowbox were not loaded.
If I click on the link (My Image1 or My Image2), the image opens in a new page and not in Ninja Shadowbox.
Also, I noticed that you use the rel attribute "lightbox" instead of "shadowbox".
This should work both ways but I recommend to use only "shadowbox".
Make sure you have Ninja Shadowbox activated/published in an existing module position from your default template.
I'm still not sure what you mean by the scrollbar is not working.
Which scrollbar do you exactly mean?
Maybe I don't understand because Ninja Shadowbox isn't working in the first place.
Let us know how it goes.