There's a plethora of potential factors that can factor in here.
To be honest, I think it would be best if you open this as a support call, and work with support from there - since a lot of this will be affected by environmental and other factors that it's not really possible to give much of a blanket statement or comparison here (It starts already with questions such as your chosen online scanner was scanning for the same files (or a reduced filelist), details on how they work, etc. etc.) ... isn't really something that can be answered in a general way I think.
The possibile reason for this are legion potentially, so needs to be looked at on a "case by case" basis.
LANDesk EMEA Technical Lead