Ok...... my biggest problem with the latest build and WB4, was when using a MyIE2 skin (which I'm discovering is able to skin more than it did previously) was the menus.... they were acting freaky!
The fix..... open the myie.ini located in the Config folder and set the PureMenuMode=1
note; close MyIE2 before editing, or the changes won't be saved.
Then I copied this to my skin.ini
[MENU_STYLE]
//Effects all drop down menus.
//Theme gives some predefined styles. Valid values are XP, DEFAULT, CUSTOM
//XP looks like office xp style. Defaut looks like the one in the previous version
//By using CUSTOM you can have more control over styles. Default value is XP.
THEME=CUSTOM
SELECTED_BK_COLOR=#bcc0d4
SELECTED_BORDER_COLOR=#E2E2E2
SELECTED_TEXT_COLOR=#000000
MOST_FAVORITE_TEXT_COLOR=#FF0000
//Use flat menu or system menu. Default is 1
FLATSTYLE=0
//unselected item
UNSELECTED_BK_COLOR=#E2E2E2
UNSELECTED_TEXT_COLOR=#000000
//disabled selected item
DISABLE_SELECTED_BK_COLOR=#F8F8FF
DISABLE_SELECTED_BORDER_COLOR=#000000
DISABLE_SELECTED_TEXT_COLOR=#9C9C9C
//disabled unselected item
//disabled unselected item bk color will be the same as unselected item background color, defined above
DISABLE_UNSELECTED_BORDER_COLOR=#F0F0F0
DISABLE_UNSELECTED_TEXT_COLOR=#9C9C9C
//Separator style. Valid values are SOLID,DASH,DOT,DASHDOT,DASHDASHDOT
//Effects Separator lines in the dropdown menus (Shortcuts, Favorites, etc.)
SEP_STYLE=DOT
SEP_COLOR=#000000
//icon space on the menu
ICON_BK_COLOR=#f0f0f0
OFFSET_ICON=0
//check box
SELECTED_CHECKBOX_COLOR=#f0f0f0
CHECKBOX_BORDER_COLOR=#F8F8FF
UNSELECTED_CHECKBOX_COLOR=#F8F8FF
DISABLED_CHECKBOX_COLOR=#f0f0f0
//Checkbox image may also be loaded from an icon file, 16*16 size
CHECKBOX_ICON=checkbox_icon.ico
DISABLED_CHECKBOX_ICON=disabled_checkbox_icon.ico
Probably a lot of settings in there that I didn't need or use, but it worked for me....... now my WB menus are being used. 
I've discovered this morning why my progress bar isn't skinned........... MyIE2 is skinning it.... and my skin has no info for it too read......... so it's rather plain. It seems that the skinning format has changed a bit, and I need to compare the old with the new to see what's different ........... (a little more coffee will be required)
I'll ask about the repaint issue on that line below the tabs, and see what Tara, and Scoooby have to say.......... it bugs me too, but obviously not as much as it bugs Chris. 