...
The skill window being up off the top of the window could be one of a few things:
1. When going back into focus (noticeable on dual monitor setups), if you click directly on a gump, it has a tendency to offset by a great deal. Usually this offset puts the gump to the far left of the cursor, but may have gone up a bit. Some gumps can be closed an reopened in the game field, others do not seem to have this corrective ability.
2. Changing resolution from a larger resolution to a smaller one. If you're running Windows at a larger resolution than you run KR when fullscreen, and then swap between them, this could happen based on where you place the gumps.
3. UI scale changing. If you go to a smaller scaled UI, place your UI gumps (menus, hotbars, backpack, etc), then set the UI scale up to a larger setting, it could place the gump outside of the screen area.
If you DO notice that a given gump does not appear when it should, go to My Documents\EA Games\Ultima Online\User Data\Account\Shard and find your character name's file. Open it in Notepad and look for any coordinates that are outside your resolution's normal range. For example, the Skills Window has the following listing:
<WindowPositions name="SkillsWindow" x="446.302185" y="544.000183" />
If the X and Y coordinates are outside your resolution's range (or has a negative value such as x="-125.894723"), set them to somewhere mid-range of your given resolution (500x500 for example for larger resolutions) and save the file. This will push the affected gump back into the window.
If more problems persist, or if you have big hotbar problems, sometimes it may be easier to simply delete the file and force the game to "rebuild" your desktop (this of course will mean you will lose any and all extra hotbars as well as items, spells, skills and macroes tied to all hotbars).
So final bit of advice, when you get your KR desktop set up as you like it, BACK UP THE USER DATA FILES just in case something happens, that way you can simply replace the file and not lose all of the setup work.