It's difficult to understand what you mean when you say you "crop the scenes top and bottom globally"... Are you referring to the Global Margins setting? This should not crop, but rather inserts blank space between each child scene. Each child scene in the crawl also has a "margins" setting on the Roll/Crawl tab that can affect the spacing individually on that scene..
If you post a link to your crawl scene it might help people to see what you are having an issue with.
#XPression