I want to echo the concern about the 'floating' top bar, but from a slightly different angle. I am slightly dyslexic and the floating toolbar aggrevates a problem I already have following the flow of text lines.
To avoid losing my place in the text, I am in the habit of focusing on a particular position within the page and then scrolling to page to see additional lines (rather than reading down the page and then scrolling a whole pageful at a time when I hit the bottom). On the old perldoc site, I was in full control over how much text scrolled into view. This is not so for the new perldoc site layout.
If there is a way to insure that the floating bar does not cut lines of text in half that might go a long way to making it more comfortable for certain readers. Otherwise, I think one should look at other ways to make "tools" accessible. Floating sidebars, perhaps?
Update:It appears the flicker in the middle is unrelated to the floating header. It also is only visible for certain usages of scrolling. To see it: keep your eye focused on the middle of the page and scroll using slide rather than page down, space or click - there is a box on the right that "wobbles", "flickers" as you scroll.
As for the floating header, if you are using firefox, you can remove it by installing the firefox extension Stylish and the style Pin the Perldoc Header down. Many, many thanks to the monks in the CB and especially hobbs who wrote the style. See perldoc.perl.org -- keep the navigation header out of your way for more information.