Thank you for your reply! It is NOT cut off in SMART notebook. I will send both files to the email you provided. Thank you!
For the workarounds..
I have realized that what happens is that it creates two images that are grouped together overlapped. So if I ungroup them, then select only one and move it then the problem is solved. This is not ideal obviously to have to do on each slide of a transitioned file.
If converted to a PDF, we can only pull in 15 slides at a time that must be manually selected. Some of our math files that come from CPM have 200 slides with it. This is simply not a feasible option.