TuneUp docks to the right of iTunes and WMP, but sometimes (in rare occasions) it won't dock successfully. If you are using iTunes, try resizing or moving the iTunes window to force TuneUp to dock.
If you are using Windows Media Player, this application can sometimes disconnect communication to its plug-ins. In these cases, you have to enable the TuneUp plug-in again in Windows Media Player.
In WMP11 or below, you can do this by clicking the View menu item, then select Plug-ins --> Other --> TuneUp
If you are using WMP12, please right click on the top bar of the player, next to where the word Library is and that will bring up the menu where you can find the Tools.
The plugin option is found in Tools --> PlugIns --> TuneUp