FBL3N gives the GL line Items, which includes GL accounts created with Cost Element as well as without Cost Element.
Whereas KSB1 includes line items which were generated for Cost Elements only.
Hence if there is a Balance Sheet Account, You will not have a Cost Element created for the same. The entry will appear in FBL3N for that account, where as you will not have it in KSB1.
Hope you got the difference.
Appreciate if you could award points if you find this information helpful.