[bestgenman]

I don't want to be too elementary so don't take offense if this post seems so.  Most Newel's are built with Square D panels and from top down #1 on the left is on one leg of the 240V incoming and #3 is on the other leg.  The left side numbering is: 1, 3, 5, 7, and so on.  The right side is 2, 4, 6, ...you get the scheme.  #1 & #2 are across from each other and on the same leg.  #3 & 4 are on the opposite leg.  

Your generator is 240/120V 3 wire , the same as the incoming from your 50A cord (if plugged to a 50A receptacle which is 240/120).  The loads on leg "A" must all be on and nothing is using leg "B".  It will be the same when the generator is on as well.  If it is not then something is amiss in your shore power side.  The quick answer is to look at the voltmeter while on shore,  Do you have voltage on both?  If so, then balance your loads (as has been mentioned).