Sorry I didn't check the .pot file, it seems that last minute changes were not included. I have attached a new atahualpa.pot file in this post. The .pot file is supposed to be the base file that is not linked to any specific language.
I have tested the attached .pot file and it seems o.k. except that it throws one error while saving for "% comments" if it's translated to "% Kommentare". Could you just save the de_DE.po regardless and see if the resulting de_DE.mo file works on a german blog?
It should work like this:
In PoEdit:
"New catalog from pot file", choose "atahualpa.pot"
Fill out "Project Info" except plural forms:
Atahualpa Deutsch or similar, Your name, Your email, German, Germany, UTF-8, UTF-8
(not sure if iso-8859-1 would be better as German "charset" but UTF-8 should cover everything?)
The other two tabs (paths, keywords) should not be required
Save as "de_DE.po" (or, whatever the Wordpress extension for the given language is:
http://codex.wordpress.org/WordPress_Localization
With PoEdit's default setting this would also create a "de_DE.mo" along with the "de_DE.po" file. "de_DE.mo" is the compiled file that would be included with the theme.
Translate and click "Save" before closing PoEdit
Unlikely but just in case:
Open de_DE.po and make sure the terms don't have paths from your local computer such as
#: C:\wordpress\theme-translations\atahualpa3\_atahualpa3.1.7/comments-paged.php:3
It should be more like this:
#: comments-paged.php:3