I actually noticed this before I updated SC on my laptop (Window 8.1 x64). Problem remained after update.
When I right-click the SC tray icon, the SC context-menu shows *behind* the taskbar, and the taskbar context-menu simultaneously displays on top.
Taskbar is on auto-hide.
No problem with other tray icons (CHS, FARR, CintaNotes, Dopus, Listary).
Previous version (I *think* it was 4.8.x):Right-click tray icon displays SC and taskbar menu
latest version, 4.9.0:Right-click tray icon displays SC and taskbar menu
the SC menu shifted a bit between versions but otherwise no difference.