Highlight box issue in Version 9

Hi, I am working on a project where the Highlight boxes are not lining up properly with what I want to highlight. 

I am on the most updated version of 9: 9.0.1.320

I haven't created a project in about 2 weeks but this has never been an issue before.

Screenshots from my Captivate project Preview (happens in Browser view as well as the regular Captivate slide preview):

So, above is how I want it to look, but to get that, I have to set up the screen to do this

Please help, I feel like I am losing my mind!