Here's something to try, Dave...
Instead of hooking up a mike, try running an mp3 player through the mike section, and turn off the VH. This might get you a better idea of whether the mike section is coloring the input.
I still think that, as Korg say the input is an unbalanced one, putting a balanced mike into it may not be the best bet. Usually, on pro gear, if an input is unbalanced, you need to convert a balanced signal to unbalanced first, and boost the gain externally. Or simply use an unbalanced mike.
My take still is that, if the mike pre and EQ are not up to snuff, turn down the input level, and use an external mike pre and EQ.
But try simply running a high quality MP3 or .WAV into the input in stereo, and then play the SAME MP3 from the Korg's MP3 player (that way, your output will color both the same). Take great care to make sure they are both at exactly the same volume (check your PA's meters) then see if the mike input is noticeably clouding the sound.
One thing about this test is, the MP3 player's outputs will be line level and flat (turn off any EQ in the player) and will hit the pre at an unbalanced level. If you don't hear any difference at this point between the input and the built-in player, then we can put it down to either the mike itself or the preamp section of the input (it will be putting on a LOT more gain than the line level outputs of the player need). At this point, you may well be stuck with using an external pre and EQ to boost the mike to line level.
But if the MP3 player sounds clouded and colored, that's basically IT... The input section is naff, and you need to start making waves over at Korg Forums, and see if Korg can't upgrade the mike in board. Chances are, it's a separate circuit board than the main board, possibly upgradeable. I doubt that the VH code itself is the issue. Even the main mike straight sounds muddy...
Remind me again what mike you are using...
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An arranger is just a tool. What matters is what you build with it..!