Are you using the Sony Reader software on your computer, and is this how you are connecting and downloading books to your reader? I believe it is automatically set to synchronize with the reader upon any connection. I suppose it would depend on how many books, etc. you have in that software as to how long it would take.
Rather than using the Sony reader software on my PC, I use the free Calibre (donations welcome), which is a much better program and allows you to control this sort of thing (mine is set to manual), as well as much more powerful features for maintaining a library. I would suggest that you consider using it; you don't have to use Sony's computer reader software to transfer books to your reader.
I haven't had my 650 for very long, but I hung around these forums for a while before I got it and set up Calibre so that it was ready to go when my PRS-650 arrived, so I've never even used the Sony reader software with my device. Thus, I have no experience with what you're talking about, and should perhaps just shut up and wait for someone familiar with the Sony PC software to show up....
