Mofi, I have tested this myself, using XP Classic theme, and looked at UltraCompare Professional 126.96.36.1990 and UEStudio, Windows Explorer, Firefox, and a more recent version of MS Office.
What I found was that the "menu highlight" item in UE is like XP's Explorer menu highlight (and Firefox), and the UltraCompare menu highlight is like that of Microsoft Word and other newer MS products. At least in XP.
By using this OS and theme, I was able to determine the underlying reason behind the menu highlighting differences. This is, at this time, MY opinion on what is actually happening, and has not been confirmed by IDM.
There is a definite difference here in how the menu highlights are drawn. In UC, it uses the menu highlight color to "outline" the menu item, then it "blends" that color with the background color for the inside color of the box, while keeping the text color of the menu item unchanged. In UE, it uses only the one highlight color for the menu item, and the text color changes in order to make it readable.
In essence, UC is "mimicking" the menu behaviors of Windows Vista and above, while UE leaves it up to the OS to determine how the menus are drawn. Because of this difference, UC isn't quite getting it right to make it identical to how the OS does it, which the UE menu seems to indicate. UC should be checking the OS version and should only do the "menu enhancement" for XP.
I know of no way to change this except to write IDM Support and let them know what is going on.