Problem solved!
I found some " in the lookup file. Looks like the splunk lookup gets in trouble if only one " is appearing per lookup-file line.
It results in strange behaviour as described above. The lines between a first single-" and the next " getting an null content.
After letting sed delete all the " in the file, the lookup works fine!
As I use a script to fill the lookup files it was easy to add the following sed command:
sed -i 's/"//g' $LOOKUP_FILE
Now every future lookup-file should be compatible.
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