Balsamiq Edit: This has been fixed in version 3.5.5
I’ve just started using Balsamiq Mockups 3 today (so excited!) and while I’m still finding my way around and setting it up so it works best for me, I have noticed that if I try to scroll to the right or left, or up or down, on the actual mockup screen, then sometimes the Navigator Pane will automatically expand to its full width. I have to keep resizing it back down to its minimal size so I can see more of the mockup. I have also noticed it happening when I’ve been selecting multiple controls at once on a mockup. It’s really annoying. I like having this pane open because it shows me the other mockups I have open (like in the old version where it was tabbed along the bottom), and I frequently have to switch between one and another, but I’m guessing for now I just need to close it until I need it, then reopen it.