I'm not sure it is the same problem, but I've just stumbled an issue with the palette view. I have the standard palettes (from yed 3.11.1 / JRE Hotspot 1.7.0_17 / WinXP, double screen 1280x1024 resolution), and if I "open" several palettes I am not able to scroll down completely, either with the mouse wheel or with the keyboard, I am "bocked" somewhere in the middle. I can scroll up completely, but not all the way down - it is as if I was "blocked" on some size. It does not seem related to the number of open palettes, but with the vertical size of the palette : if I only open a small palette, scrolling down works. And now I restart yEd, and the bug disappears :-(
I had opened yEd, created a new graph with only a few nodes, and the problem appeared. This is the first time I see it, I'd update here if I can reproduce it (note also I updated to yed 3.11.1 somewhat recently. I'd guess my JRE has been the same for some time, but not sure)