Scroll BarsThe comments in this section apply to all programs running in Lion, whether or not they have been recompiled for Lion.
There are two kinds of scroll bars in Lion, called "legacy scrollbars" and "overlay scroll bars". Legacy scroll bars are the old scroll bars from earlier versions of OS X. Their color in Lion is more subdued, and the arrow buttons on scroll bars have disappeared, but can be simulated by holding down the option key while scrolling. These changes are in line with Apple's goal of emphasizing content and deemphasizing tools used to manipulate content.
Overlay scroll bars come from the iPhone and iPad. When a window has overlay scroll bars, its contents fill the entire window to the edges. To scroll, directly push the window's contents. When that happens, scroll bars will temporarily appear on top of the contents, and it is possible to move the mouse to those bars and scroll in the old way. Directly move the contents for small moves, but use the bars when you want to rapidly get to another part of the document.
In overlay scrolling, scroll bars do not appear if you hover over the edge of the window. That wouldn't make sense because the contents goes to the edge and you might just want to click on those contents. Scroll bars only appear if you start directly scrolling the window's contents.
Suppose TeXShop is running on a desktop machine with a fairly old mouse. Then pushing on the contents of the source window will select lines of text rather than scrolling the contents, so overlay scroll bars won't work in the source window. In the case of the preview window, directly scrolling the contents works if the hand tool is selected, but doesn't work if the text tool or magnify tool is selected. So in either case, overlay scroll bars won't work.
On the other hand, if TeXShop is running on a portable with a gesture-aware trackpad, then overlay scroll bars will work. For instance, swiping with one finger selects text in the source window, but swiping with two fingers scrolls.
Scrollbar behavior on Lion is determined by the General Control Pane in Apple preferences. Users can select to always use legacy scrollbars, or always use virtual scroll bars. But the default choice is to let Apple choose based on your input devices. If you have a desktop machine with an old mouse, you get legacy scroll bars. If you have a modern portable, you get overlay scroll bars. If you have a trackpad, or a Mighty Mouse, or a mouse with a scroll wheel, I don't know. Luckily, Apple decides.
At WWDC I had a portable, and I noticed the TeXShop used virtual scroll bars. Later back home, I ran Lion on a desktop machine and saw legacy scroll bars, so I thought ``Apple changed their mind for the golden master.'' It wasn't until I watched a video from a session I missed at WWDC that I understood what was happening. Not too swift on the uptake.