I think that I have found the cause.

If you use gconf-editor and navigate to the key
"/apps/gedit-2/preferences/encodings/auto_detected" then you will see a
chain of encodings which are considered during auto detection.  When I
did so, I could see that any encodings for the Czech language were
missing even though I had installed complete Czech language support via
System -> Administration -> Language support.

1) Workaroud:
----------------------
a) find the right encodings:
Start gedit -> Open -> Character encoding "button-list" -> Add and Remove. Here 
you can add encodings that will be added to the "button-list". Select and add 
all that you intend to use. Then press OK and then close gedit.

b) add the encodings to the autodetection key:
Start the gconf-editor, search for 
"/apps/gedit-2/preferences/encodings/auto_detected". Under the key 
"auto_detected" in the key "shown_in_menu" you will see all encodings that you 
added in the previous step. So, double click the key  "auto_detected" and add 
the same encondings to this key. Then you can sort them e.g. like "UTF-8, <your 
encodings>,<rest of all starting with the CURRENT>"

That is all. For me it works well.


2) BugFix
----------------------

I assume that local encodings relating to a language installed through
the language support should be automatically added to those two encoding
keys of gedit, because the user probably writes and reads in more
languages and will need it.

-- 
Gedit encoding autodetection fails on all cp1250 files
https://bugs.launchpad.net/bugs/289939
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