We have had similar reports in the past (see e.g. BUG: Palette is not properly scorrallble or Palette scrolling gets stuck). Unfortunately, we have had no luck yet in finding the root cause of the problem.
If this problem occurs, save your current work and restart yEd. Instead of restarting yEd, hiding and unhiding a palette section (in "Edit" -> "Manage Palette") usually fixes the issue as well.