We believe that your issue has been closed by the upload of
Version 1.1.13 of grml-etc from Michael Prokop <mika@grml.org>.
The explanation is attached below

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Format: 1.8
Date: Mon, 06 Apr 2009 11:45:44 +0200
Source: grml-etc
Binary: grml-etc
Architecture: source all
Version: 1.1.13
Distribution: unstable
Urgency: low
Maintainer: Michael Prokop <mika@grml.org>
Changed-By: Michael Prokop <mika@grml.org>
Description: 
 grml-etc   - ecetera files for the grml system
Changes: 
 grml-etc (1.1.13) unstable; urgency=low
 .
   * /etc/skel/.ipython/ipythonrc: Do not activate the
     IPython.Extensions.InterpreterExec module by default anymore.
     Upstream does not ship this configuration snippet as well.
     Thanks for reporting and debugging, wuehlmaus! [Closes: issue618]
   * /etc/skel/.Xresources: improve xterm/ uxterm font setup.
     This should fix our longstanding unicode problem. Thanks to
     Thorsten Glaser for help. [Closes: issue468]
     Additionally add configuration for urxvt.
   * /etc/skel/.Xmodmap: Use 'EuroSign' instead of 'currency'.
   * Debian postrm:
     - when removing the package use /etc/init.d/rc instead
       of /etc/init.d/grml-[reboot|halt].
     - make sure the ssh init script even exists if something is failing
   * Slightly improve message for removing media from tray on reboot/halt.
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I'm still not sure how to proceed with this issue. :-/

Our defaults, vs.

uxterm -fn '-misc-fixed-medium-r-semicondensed-*-*-120-*-*-*-*-iso10646-1'

vs.

uxterm -fn -misc-fixed-medium-r-normal--18-120-100-100-c-90-iso10646-1 -fw -
misc-fixed-medium-r-normal-ko-18-120-100-100-c-180-iso10646-1

vs. .....?

Alright, finally I could reproduce this issue. See http://grml.org/tmp/
Xresources.txt for a working setup, though I really don't like the big font 
look'n'feel changes. I'm still not yet sure what we should do to resolve this 
issue.

Credits for bugreport and additional information to Matej Rehak:

I get correct national characters only if using the "Huge" size in uxterm, 
other sizes are messed up. I can also force uxterm to use other font at 
startup, so that the startup font/charset is correct, too:

uxterm -fn '-misc-fixed-medium-r-semicondensed-*-*-120-*-*-*-*-iso10646-1'

But as I've written in my previous mail - gvim has no font/charset problems 
(with default font). gmplayer with default font (Sans) displays (in subtitles) 
'_' instead of national characters (but it displays correct vowels áéíóúý, 
which are part of ISO-8859-1), but when setting its font to "DeJaVu Sans", the 
problem is solved :-)

I've simply written all Slovak/Czech characters (small & capital) in 3 lines:
1: small letters - stripped diacritics
2: small letters with diacritics
3: capital letters with diacritics
It's in UTF-8 encoding, UNIX line breaks.
I've also included a screenshot - how should it look like in text
editor -- try vim in uxterm, different uxterm font sizes.