Console display annoyance

I have an annoying problem with console windows in that they show
up with the last row being partly obscured (like half a row).
The scrollbar area on the right also doesn't seem to paint properly
with a small area between the scrollbar and console area picking up
whatever's underneath (program or desktop).

I've done all kinds of things regarding per application settings
such as using UIS1 version of a skin, disable skinning of scrollbars,
titlebar only, etc.

What I've noticed is that cmd will show up fine as well as any
other console app who's shortcut calls just its executable (FAR file
manager, Links browser, etc.) but once a program is run within
the window the mess up occurs. Or if the console window starts up
via batch or extra commands.
Note: FAR and Links (among others) have Screen Buffer Size and
Window Size set to a fixed size so no scrollbars are used.

Examples:
1) cmd.exe looks good. If I start say Edit or Vim I see the console
window shorten a bit (the scrollbars also disappear - I suppose
something is smart enough to know they don't need any?).
A 4NT window is also fine 'til something is run like its internal
LIST command.
With some themes I noticed that running a program will shorten
the console window enough to totally remove the last couple of
rows. No command line visible at all.

2) Lynx browser status line is almost unreadable. Shortcut calls
batch file (was .bat, now .cmd).

3) Bash, tcsh, korn shell windows start in a messed up state as there
are extra commands in their shortcuts.
[Shells used in Services For UNIX environment)

As a command line kind of person it makes it hard to function
at times. Usually I'll pull down the window just a tad to expose
the full prompt just to have it mess up again as soon as a command
is run.

Any ideas on what settings to use to fix this, if at all possible?
Thanks,
Marc

P.S. Image may not be immediately available as I exceeded my transfer
rate clearing out some space.

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