Having studied engineering myself, I think its more of a matter of perception. This is my own opinion so feel free to trash it.
Business schools gauge applicants through the applications and essays. I think engineering applicants focus heavily on their analytical skills through the very nature of their jobs (engineering jobs often have lesser team and business interaction compared to other industries). Moreover managerial skills dont usually come with engineering jobs, especially at the entry level. After a few years of work, the managerial skills come to play as you get to be in charge of projects and do some solid decision making. For example, if you were an entry level civil engineer, you would be doing a lot of field work, estimations, valuations, site survey. You tend to work solo, with little interaction with other groups or teams and you report to a supervisor, and then after a few years (usually 4-5), you would be in charge of your own projects.
Now compare this to a fresh graduate who works in finance or management. While the analytical skills are strongly required, there is more need for business and leadership skills, since the majority of finance jobs require interaction at all levels. You have to work with the analyst, associate, director or even the CFO (rare in big firms) on several projects.
This is just a hypothesis. So, when you present this on paper, through your application or essays, a student with an engineering background loses out to folks from other industries, since the analytical part is top heavy while the business or leadership segment is weak.
Yes, there are several exceptions, but I guess this is one way of looking at it.
Just my 2 cents.